title: Methylation_EPIC_sample25

value: E

tag: pedigreeid


title: Methylation_EPIC_sample18

status: Public on Aug 04 2022

type: genomic

city: Ann Arbor

first: Lulu

last: Shang

state: Michigan

address: 1415 Washington Heights

department: Biostatistics

country: USA

institute: University of Michigan

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to IIllumina Infinium HumanMethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: For each chip, the Minfi R package was used to perform background correction and normalization. The regression on correlated probes (RCP) method was then used to adjust probe-type bias.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood leukocytes

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from stored peripheral blood leukocytes using AutoGen FlexStar (AutoGen, Holliston, MA) and DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA)

tag: race

value: African American (AA)

tag: gender

value: F

tag: age(yrs)

tag: plate

tag: column

tag: row

value: G

tag: subjectid

tag: phase


title: P-2687_S-2688

type: SRA

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

library_source: transcriptomic single cell

data_processing:
Cell Ranger (10x Genomics) was used with default parameters to demultiplex reads and align sequencing reads to the genome, distinguish cells from background, and obtain gene counts per cell.
Alignment was performed using the hg19 reference genome build, coupled with the Ensembl transcriptome (v75). In the case of snRNAseq, reads mapping to intronic regions were included.
Assembly: hg19
Supplementary files format and content: README_scRNA.md: markdown file containing information on the metadata, barcodes, features and matrix files.
Supplementary files format and content: *__features.tsv.gz, *__barcodes.tsv.gz,  *__matrix.mtx.gz: compressed filtered features, barcodes and expression matrices generated by Cell Ranger.
Supplementary files format and content: *.metadata.NG2022.tsv: Tab-separated file containing info for each cell.

molecule: total RNA

source_name: tumor

extract_protocol:
Fresh tumors collected after surgery were enzymatically digested and mechanically dissociated using the papain version of the Brain Tumor Dissociation kit (Miltenyi Biotech) or the Worthington Papain dissociation kit. Red blood cells were lysed by ammonium chloride treatment for 5 min on ice. Cell viability was assessed with Trypan Blue. For samples with low viability (< 60%), dissociated cells were enriched for live cells using the Dead Cell Removal kit (Miltenyi Biotech).
Cell capture and library preparation was performed according to the Chromium Single Cell 3’ (v3) protocol.

tag: tissue

value: tumor

tag: Sex

value: female

tag: age (years)

tag: location

value: brainstem

tag: diagnosis

value: high-grade glioma

tag: cellranger version(processing)

tag: technology

value: 10X Chromium Single Nuclei 3'


title: exp1_r2_hrs04-08_b1_L001

city: Seattle

first: Diego

last: Calderon

address: 3720 15th Ave NE

institute: University of Washington

library_source: genomic

data_processing:
The sci-ATAC-seq3 raw reads were processed using the pipeline described in (Domcke et al. 2020). Reads were mapped to the dm6 reference genome. The non-duplicate fragments are used for peak calling with MACS2 (Zhang et al. 2008) in each sample, and then merged together with bedtools (Quinlan and Hall 2010). We generate sparse matrices counting reads falling into the merged peak set for cells passing a sample-specific threshold for each sample.
Genome_build: dm6
Supplementary_files_format_and_content: MM sparse matrix containing the sci-ATAC-seq read count for peaks (rows) by nuclei (cols).

organism: Drosophila melanogaster

source_name: whole embryo

extract_protocol:
Drosophila melanogaster embryos were collected as previously described (Sandmann, Jakobsen, and Furlong 2006; Cusanovich et al. 2018).
To create the sci-ATAC-seq3 libraries, we followed the protocol from (Domcke et al. 2020).

tag: developmental stage

value: Drosophila embryo (0-20 hrs)


title: P-3198_S-3199

value: male

value: brain


title: Methylation_450k_sample181

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to IIllumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

value: M

tag: pedigreeid


title: Methylation_450k_sample182

tag: race


title: exp1_r2_hrs03-07_b1_L004


title: Methylation_EPIC_sample16

tag: gender

value: H


title: P-2077_S-2077

value: fourth ventricule

value: Ependymoma


title: Methylation_EPIC_sample17

tag: age(yrs)


title: Methylation_EPIC_sample22

tag: plate


title: exp1_r2_hrs03-07_b1_L003


title: Methylation_EPIC_sample15

tag: column


title: Methylation_450k_sample179

tag: row


title: Methylation_450k_sample180

value: D

tag: subjectid


title: exp1_r2_hrs03-07_b1_L002


title: P-1764_S-1766


title: Methylation_EPIC_sample14

tag: phase


title: Methylation_450k_sample178

value: C


title: P-1741_S-2756

tag: tissue


title: Methylation_450k_sample177

value: African American (AA)

value: E


title: exp1_r2_hrs03-07_b1_L001


title: Methylation_450k_sample176

value: F


title: exp1_r2_GM+CH12.barnyard_b1_L004


title: Methylation_EPIC_sample13


title: P-1713_S-1713

value: tumor

tag: Sex


title: P-1775_S-1775

value: female

tag: age (years)


title: Methylation_EPIC_sample12


title: exp1_r2_GM+CH12.barnyard_b1_L003


title: P-1569_S-1569

tag: location

value: cortex


title: Methylation_EPIC_sample11


title: Methylation_450k_sample174


title: exp1_r2_GM+CH12.barnyard_b1_L002


title: P-1190_S-1197

value: Parieto-Occipital lobe

tag: diagnosis

value: high-grade glioma


title: exp1_r2_GM+CH12.barnyard_b1_L001

value: Drosophila embryo (0-20 hrs)


title: Methylation_EPIC_sample10

value: B


title: Methylation_450k_sample172


title: Methylation_450k_sample173


title: exp1_r1_hrs16-20_b1_L004


title: Methylation_EPIC_sample9

value: A


title: BT2016062

value: male

value: Posterior fossa

tag: cellranger version(processing)

value: 10X Chromium Single Cell 3'


title: BT2018022

value: Ependymoma

tag: technology


title: exp1_r1_hrs16-20_b1_L003

tag: developmental stage


title: Methylation_EPIC_sample8

value: M

value: H

tag: pedigreeid


title: Methylation_EPIC_sample7

tag: race

value: African American (AA)

value: G


title: exp1_r1_hrs16-20_b1_L002


title: Methylation_EPIC_sample6

tag: gender

value: F


title: exp1_r1_hrs16-20_b1_L001


title: exp1_r1_hrs14-16_b1_L004


title: Methylation_450k_sample171

tag: age(yrs)


title: Methylation_EPIC_sample5

tag: plate

value: E


title: Methylation_450k_sample170

tag: column

value: C


title: Methylation_450k_sample169

tag: row


title: Topo1cc_E2_1h_exp1

city: La Jolla

first: Yuliang

last: Tan

state: California

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

data_processing:
Library strategy: CUT&RUN
Basecalls performed using CASAVA version 1.4
reads were aligned to the hg38 genome assembly using Bowtie version 2.0.1.
Genome_build: hg38
Supplementary_files_format_and_content: bed and bedgraph

source_name: MCF7 cells

growth_protocol: MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen). LNCAP cells were maintained at 37°C and 5% CO2 in Advanced RPMI 1640 medium (GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen).

extract_protocol:
CUT&RUN was performed using CUTANA™ CUT&RUN Protocol [www.epicypher.com] which is an optimized version of that previously described. For each sample, 5x105 cells were immobilized onto Concanavalin-A beads (EpiCypher #21-1401) and incubated overnight (4ºC with gentle rocking) with 0.5 µg of antibody.
CUT&RUN enriched DNA was purified, and 10 ng used to prepare sequencing libraries with the KAPA HTP/LTP Library Preparation Kits

treatment_protocol: For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM. TNFalpha(R&D systems) was added to a final concentration of 20 ng/ml. 5α-dihydrotestosterone (DHT, Sigma) was added to a final concentration of 100 nM. The ethanol (EtOH) vehicle control was 0.05% in all samples.

tag: cell line

tag: cell type

value: human breast cancer cells

tag: treatment

tag: chip antibody

value: TopoGEN TG2017-2 (Lot# 17AG15)


title: Topo1cc_E2_1h_exp2


title: Topo1cc_Veh_exp1

value: Vehicle


title: Methylation_450k_sample175

tag: subjectid

tag: phase


title: Topo1cc_Veh_exp2


title: exp1_r1_hrs14-16_b1_L003

value: Drosophila embryo (0-20 hrs)


title: Methylation_EPIC_sample4

value: D


title: exp1_r1_hrs14-16_b1_L002


title: Methylation_450k_sample167


title: Methylation_EPIC_sample3


title: exp1_r1_hrs14-16_b1_L001


title: Methylation_450k_sample166

value: A


title: Methylation_EPIC_sample2

value: B


title: Methylation_EPIC_sample1


title: exp1_r1_hrs12-16_b1_L004


title: Methylation_450k_sample164


title: exp1_r1_hrs12-16_b1_L003


title: Methylation_450k_sample168


title: Methylation_450k_sample163


title: P-6519_S-9084

tag: tissue

value: tumor

tag: Sex

value: male

tag: age (years)

tag: location

value: pons

tag: diagnosis

value: high-grade glioma


title: Methylation_450k_sample162

tag: race

tag: pedigreeid


title: Ku70_Veh_exp1

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the hg38 genome assembly using Bowtie2.
Genome_build: hg38
Supplementary_files_format_and_content: bed and bedgraph

extract_protocol:
Cells were cross-linked with 1% formaldehyde at room temperature for 10 min. And then the cross-linking was quenched with 0.125M glycine for 5 min. Chromatin was fragmented using a Bioruptor® Pico (Diagenode) for 10 min at high power, with an interval of 30 s between pulses to get around 200bp fragments and precleared using 20 μl Protein G Dynabeads (Life Technologies, Cat# 10009D). Subsequently, the soluble chromatin was incubated with 2-5 μg antibodies at 4°C overnight. Immunoprecipitated complexes were collected using 30 μl Protein G Dynabeads, which have been saturated with PBS/1% BSA over night at 4°C, per reaction. For all ChIPs, after de-crosslinking overnight at 65°C, final ChIP DNA was extracted and purified using QIAquick spin columns (QIAGEN).
The libraries were constructed following Illumina’s Chip-Seq Sample prep kit.

value: Veh

tag: antibody


title: exp1_r1_hrs10-14_b1_L004

tag: developmental stage


title: Ku70_Veh_exp3


title: exp1_r1_hrs12-16_b1_L001


title: Ku70_E2_1h_exp3


title: Ku70_E2_1h_exp1


title: Methylation_450k_sample161

value: African American (AA)

tag: gender

tag: age(yrs)

tag: plate

tag: column


title: HP1g_Veh_siNC_exp5

tag: cell line

tag: cell type

tag: treatment


title: P-3200_S-3867

value: left frontal lobe

tag: cellranger version(processing)

tag: technology

value: 10X Chromium Single Nuclei 3'


title: HP1g_Veh_siKu70_exp5


title: Methylation_450k_sample159

value: M

tag: row

value: E

tag: subjectid

tag: phase


title: Methylation_450k_sample160

value: F

value: H


title: exp1_r1_hrs10-14_b1_L003


title: Methylation_450k_sample165


title: exp1_r1_hrs10-14_b1_L002


title: P-1969_S-3584

tag: tissue

tag: Sex

tag: age (years)

tag: location

value: Parietal lobe

tag: diagnosis


title: HP1g_Veh_exp3

value: human breast cancer cells

tag: antibody


title: Methylation_450k_sample158

tag: race

tag: gender

tag: age(yrs)

value: G

tag: pedigreeid


title: HP1g_Veh_exp2

tag: cell line

tag: cell type


title: exp1_r1_hrs10-14_b1_L001

tag: developmental stage

value: Drosophila embryo (0-20 hrs)


title: exp1_r1_hrs12-16_b1_L002


title: P-6640_S-9581

value: thalamus

tag: cellranger version(processing)

tag: technology

value: 10X Chromium Single Cell 3'


title: HP1gS83D_E2_1h_exp2

tag: treatment


title: P-6331_S-8904

value: tumor

value: male

value: brain


title: exp1_r1_hrs08-12_b1_L004


title: Methylation_450k_sample157

tag: plate

tag: column

tag: row

value: D

tag: subjectid

tag: phase


title: P-6337_S-8821_multiome ATAC

data_processing:
Cell Ranger ARC v2.0.0 (10x Genomics) was used (‘count’ option with default parameters) to filter and align raw reads, identify transposase cut sites, detect accessible chromatin peaks, call cells and generate raw count matrices for scMultiome samples.
Sequencing reads were aligned to the hg19 genome, coupled with the Gencode v28 (Ensembl 92) gene annotation.
For visualization of chromatin accessibility in subsets of cells, BAM files from ATAC data were subsetted using the subset-bam utility from 10x Genomics (v1.1). Pseudo-bulk bigwig tracks were generated from subsetted BAMs with a bin size of 1 and RPKM normalization using the deeptools bamCoverage functionality (v3.5.0).
Assembly: hg19
Supplementary files format and content: README_scMultiome.md: markdown file containing information on the metadata, barcodes, features and matrix files.
Supplementary files format and content: *__features.tsv.gz, *__barcodes.tsv.gz,  *__matrix.mtx.gz: compressed filtered features, barcodes and expression matrices generated by Cell Ranger.
Supplementary files format and content: *.metadata.NG2022.tsv: Tab-separated file containing info for each cell.
Supplementary files format and content: *.bw: bigwig files, read coverage over the human genome

extract_protocol:
scMultiome nuclei were prepared using either standard manual nuclei preparation or automated nuclei preparation. Samples subjected to automated nuclei prep were processed following the Singulator S100 protocol (S2 Genomics). Nuclei were isolated using the Nuclei Isolation kit and Singulator S100 instrument from S2 Genomics. Briefly, 5-20 mg of frozen tissue were put in a pre-cooled nuclei isolation cartridge with RNAse inhibitors. Samples were then processed on the Singulator S100 following the “extended nuclei” protocol. After nuclei prep, nuclei were centrifuged and washed twice in Diluted Nuclei Buffer (10x Genomics) and counted with the ReadyProbes Cell Viability Blue/Green kit (ThermoFisher Scientific). 20,000 nuclei/sample were loaded on the Chromium Controller (10x Genomics).
Library preparation was prepared following the manufacturer’s instructions (Next GEM Single Cell Multiome).
scMultiome (ATAC + RNA)

tag: tissue

tag: Sex

tag: age (years)

tag: location

value: pons

tag: diagnosis

value: high-grade glioma

value: 10X Chromium Single Cell Multiome ATAC + RNA


title: HP1gS83D_E2_1h_exp1

tag: antibody


title: Methylation_450k_sample155

tag: race

value: African American (AA)

tag: gender

tag: age(yrs)

tag: pedigreeid


title: HP1gS83A_E2_1h_exp2

tag: cell line

tag: cell type


title: Methylation_450k_sample154

tag: plate


title: exp1_r1_hrs08-12_b1_L003

tag: developmental stage


title: exp1_r1_hrs08-12_b1_L001


title: Methylation_450k_sample156

tag: column

tag: row

value: C


title: exp1_r1_hrs08-12_b1_L002


title: P-1780_S-1780_multiome ATAC

value: female

tag: cellranger version(processing)

tag: technology


title: P-1779_S-1781_multiome ATAC

tag: tissue

tag: Sex


title: P-6253_S-8498_multiome ATAC

tag: age (years)

tag: location


title: P-6774_S-10146_multiome ATAC

tag: diagnosis


title: HP1g_E2_1h_siNC_exp5

tag: treatment

tag: antibody


title: exp1_r1_hrs06-10_b1_L004


title: P-6640_S-9581_multiome ATAC


title: HP1g_E2_1h_siKu70_exp5


title: Methylation_450k_sample153

tag: race

tag: gender

value: F

tag: age(yrs)

tag: subjectid

tag: phase


title: exp1_r1_hrs06-10_b1_L003

tag: developmental stage


title: Methylation_450k_sample151

tag: plate

tag: column

value: E

tag: pedigreeid


title: exp1_r1_hrs06-10_b1_L002


title: HP1g_E2_1h_exp3

tag: cell line

tag: cell type

value: human breast cancer cells


title: P-1709_S-1709_multiome ATAC

tag: tissue

tag: Sex

value: fourth ventricle

tag: cellranger version(processing)

tag: technology


title: P-1701_S-1701_multiome ATAC

tag: age (years)

tag: location

tag: diagnosis


title: HP1g_E2_1h_exp2

tag: treatment

tag: antibody


title: HP1gS83A_E2_1h_exp1


title: Methylation_450k_sample150

tag: race

tag: gender

tag: age(yrs)

tag: row

value: B

tag: subjectid


title: exp1_r1_hrs06-10_b1_L001

tag: developmental stage

value: Drosophila embryo (0-20 hrs)


title: exp1_r1_hrs04-08_b1_L004


title: exp1_r1_hrs04-08_b1_L003


title: Methylation_450k_sample152

value: M

tag: plate

tag: column

tag: pedigreeid

tag: phase


title: Methylation_450k_sample148

value: A


title: P-6774_S-10146_multiome RNA

tag: tissue

value: tumor

tag: Sex

tag: cellranger version(processing)


title: P-1764_S-1766_multiome ATAC

tag: age (years)

tag: location

tag: technology


title: HP1g_E2_14h_exp2

tag: cell line

tag: cell type

tag: treatment

tag: antibody


title: HP1g_E2_14h_exp3


title: Methylation_450k_sample149

tag: race

tag: gender

tag: age(yrs)

tag: row


title: Methylation_450k_sample147

tag: plate

tag: column

tag: subjectid


title: P-6337_S-8821_multiome RNA

tag: tissue

value: male

tag: diagnosis


title: exp1_r1_hrs04-08_b1_L002

tag: developmental stage


title: Methylation_450k_sample146

value: H

tag: pedigreeid

tag: phase


title: Gata3_Veh_siHP1g_exp2

value: Santa Cruz Biotechnology sc-268 (Lot#J0515)


title: P-6640_S-9581_multiome RNA

tag: Sex

tag: age (years)

tag: location

value: thalamus

value: high-grade glioma

tag: cellranger version(processing)

tag: technology


title: Gata3_Veh_siNC_exp2

tag: cell line

tag: cell type

tag: treatment

tag: antibody


title: exp1_r1_hrs04-08_b1_L001


title: P-6253_S-8498_multiome RNA

value: pons

value: 10X Chromium Single Cell Multiome ATAC + RNA


title: exp1_r1_hrs03-07_b1_L004


title: Methylation_450k_sample145

tag: race

value: African American (AA)

tag: gender

tag: age(yrs)

tag: plate

tag: row


title: Gata3_E2_1h_siNC_exp2


title: P-1780_S-1780_multiome RNA

tag: tissue

value: female

tag: diagnosis


title: Gata3_E2_1h_siHP1g_exp2


title: P-1694_S-1694_multiome ATAC


title: Methylation_450k_sample144

value: F

tag: column

tag: pedigreeid

tag: subjectid

tag: phase


title: exp1_r1_hrs03-07_b1_L003

tag: developmental stage


title: P-1779_S-1781_multiome RNA

tag: Sex

tag: age (years)

tag: location

tag: cellranger version(processing)

tag: technology


title: Methylation_450k_sample143

tag: race


title: Input siDDX5/17 R3

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

country: France

institute: I-Stem

description: Replicate 3

data_processing:
High throughput sequencing of 50 bp single-end reads was carried out on an Illumina HiSeq 4000 platform.
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
The approach is similar to a standard ChIP-seq analysis, except that the presence of a defined amount of exogenous chromatin (from Drosophila) in each sample allows a normalization of the experimental samples and thus a more accurate comparison of RNAPII occupancy across samples. After trimming and removing adaptors, reads were then competitively mapped on a concatenation of the two genomes (the reference human genome hg19, and the calibration drosophila genome dm6) and assigned to their corresponding genome. Calibration of the read coverage was then performed for each nucleotide position.
Details of the Nextflow pipeline are available in the following GitHub repository: https://gitbio.ens-lyon.fr/LBMC/Bernard/quantitative-nucleosome-analysis/  (tag qChIPseq_polII_cbourgeois https://gitbio.ens-lyon.fr/LBMC/Bernard/quantitative-nucleosome-analysis/-/tags/qChIPseq_polII_cbourgeois and instructions in README_quantitativ-chip.md
Genome_build: hg19
Supplementary_files_format_and_content: BigWigs files

source_name: Neuroblastoma SH-SY5Y cell line (ECACC)

growth_protocol: Cells were cultured in 4,5 g/L Glucose DMEM/F-12 (ThermoFischer Scientific) supplemented with 10% (v/v) fetal bovine serum (ThermoFischer Scientific), and 2 mM L-Glutamine (ThermoFischer Scientific) in 5% CO2 at 37°C.

extract_protocol:
For each of the 3 replicates of calibrated RNAPII ChIP-seq, we pooled 4 independent IP, each of them performed on 40 µg of chromatin supplemented with 32 ng of Drosophila spike-in chromatin (Active Motif #53083), with 4 µg of mouse anti-Pol II F-12 antibody (F-12, sc55492, Santa Cruz) and 2 µg of spike-in antibody (Active Motif #61686).
Libraries and sequencing was performed by the GenomEast platform (Illkirch, France). ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode, Seraing, Belgium), according to manufacturer's instructions.

treatment_protocol: Cells were transfected for 48h with siRNAs at a final concentration of 20 nM with lipofectamine RNAimax (ThermoFischer Scientific).

tag: cell line

tag: transfected sirna

value: siRNA anti-DDX5/DDX17

tag: extract

value: Chromatin extract (input)


title: exp1_r1_hrs03-07_b1_L002


title: Input Ctrl R3

description: Replicate 3

value: Negative control siRNA anti-luciferase


title: P-1764_S-1766_multiome RNA


title: Methylation_450k_sample142

tag: gender

tag: age(yrs)

tag: plate

tag: row

value: B


title: exp1_r1_GM+CH12.barnyard_b1_L004

value: Drosophila embryo (0-20 hrs)


title: exp1_r1_hrs03-07_b1_L001


title: Methylation_450k_sample141

tag: column

value: G

tag: pedigreeid


title: IP RNAPII siDDX5/17 R3

description: Replicate 3

value: RNA Pol II IP (F12 antibody)


title: P-1709_S-1709_multiome RNA

tag: tissue

value: tumor

value: male

value: fourth ventricle

tag: diagnosis


title: IP RNAPII Ctrl R3

description: Replicate 3


title: P-1701_S-1701_multiome RNA

tag: Sex


title: Input siDDX5/17 R2

description: Replicate 2


title: P-1694_S-1694_multiome RNA

tag: age (years)


title: Methylation_450k_sample140

value: M

value: A

tag: subjectid

tag: phase


title: exp1_r1_GM+CH12.barnyard_b1_L002

tag: developmental stage


title: Methylation_450k_sample139

tag: race


title: Methylation_450k_sample138

value: H


title: P-6255_S-8500_ATAC

library_source: transcriptomic

data_processing:
Cell Ranger ATAC v1.1.0 was used (‘count’ option with default parameters) to filter and align raw reads, identify transposase cut sites, detect accessible chromatin peaks, call cells and generate raw count matrices for the scATAC samples.
Sequencing reads were aligned to the hg19 genome, coupled with the Gencode v28 (Ensembl 92) gene annotation.
For visualization of chromatin accessibility in subsets of cells, BAM files were subsetted using the subset-bam utility from 10x Genomics (v1.1). Pseudo-bulk bigwig tracks were generated from subsetted BAMs with a bin size of 1 and RPKM normalization using the deeptools bamCoverage functionality (v3.5.0).
Assembly: hg19
Supplementary files format and content: README_scATAC.md: markdown file containing information on the metadata, barcodes, peaks and matrix files.
Supplementary files format and content: *__peaks.bed.gz, *__barcodes.tsv.gz,  *__matrix.mtx.gz: compressed filtered peaks, barcodes and expression matrices generated by Cell Ranger.
Supplementary files format and content: *.metadata.NG2022.tsv: Tab-separated file containing info for each cell.
Supplementary files format and content: *.bw: bigwig files, read coverage over the human genome

extract_protocol:
Fresh tumors collected after surgery were enzymatically digested and mechanically dissociated using the papain version of the Brain Tumor Dissociation kit (Miltenyi Biotech) or the Worthington Papain dissociation kit. Red blood cells were lysed by ammonium chloride treatment for 5 min on ice. Cell viability was assessed with Trypan Blue. For samples with low viability (< 60%), dissociated cells were enriched for live cells using the Dead Cell Removal kit (Miltenyi Biotech). Approximately 10,000 dissociated cells per sample were loaded on the 10x Genomics Chromium controller.
Cell capture and library preparation was performed according to the Chromium Single Cell ATAC (v1) protocol

tag: location

value: brainstem

value: high-grade glioma

tag: cellranger version(processing)

tag: technology

value: 10X Chromium Single Nuclei 3'


title: exp1_r1_GM+CH12.barnyard_b1_L003


title: exp1_r1_GM+CH12.barnyard_b1_L001


title: IP RNAPII siDDX5/17 R2

description: Replicate 2

tag: cell line

tag: transfected sirna

tag: extract


title: Methylation_450k_sample137

value: African American (AA)

tag: gender

value: F

tag: age(yrs)

tag: plate

tag: row

value: E


title: Input Ctrl R2

description: Replicate 2

value: Negative control siRNA anti-luciferase

value: Chromatin extract (input)


title: IP RNAPII Ctrl R2

description: Replicate 2


title: P-2687_S-2688_ATAC

tag: tissue

value: female

tag: diagnosis


title: Methylation_450k_sample136

tag: column

value: G

tag: pedigreeid


title: Input siDDX5/17 R1

description: Replicate 1

value: siRNA anti-DDX5/DDX17


title: Methylation_450k_sample135

value: D

tag: subjectid

tag: phase


title: P-1764_S-1766_ATAC

value: tumor

tag: Sex

tag: age (years)

value: pons


title: Methylation_450k_sample134

tag: race

value: M


title: IP RNAPII siDDX5/17 R1

description: Replicate 1

value: RNA Pol II IP (F12 antibody)


title: Input Ctrl R1

description: Replicate 1


title: TILAC_S2_s6GCntl

city: West Haven

first: Matthew

last: Simon

state: Connecticut

address: PO Box 27392

department: Molecular Biophysics and Biochemistry

institute: Yale University

description: Reads filtered for number of T-to-C mutations (0-5+), G-to-A mutations (0-5+) and strandedness (min/pos)

data_processing:
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
Reads were aligned to the GRCh38 genome or dm6 genome using HISAT2 aligned with default parameters and --mp 4,2 .
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C and G-to-A mutations were identified using Rsamtools and a custom R script (available upon request). Only mutations at positions with a base quality score of greater than 45 that were at least three nt from the end of the read were counted.
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C and G-to-A SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C or G-to-A mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C or G-to-A mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph).
Tracks were converted to binary format using IGVtools (toTDF).
Genome_build: GRCh38 or dm6
Supplementary_files_format_and_content: TDF

source_name: Drosophila Schneider 2 cells

growth_protocol: 293T were grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco) and Pen/Strep (50 U/ml). S2 cells were grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco) and Pen/Strep (50 U/ml). 293T cell cultures were maintained at 37℃. S2 cell cultures were maintained at 27℃.

extract_protocol:
RNA was harvested by two different protocols. For normal RNA sequencing, cells were resuspended in Trizol reagent, followed by chloroform extraction and isopropanol precipitation of the RNA. Genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. Total RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018 and Kiefer et al. Journal of the American Chemical Society 2018. To isolate RNA from untreated polysome fractions, each fraction went through 1 phenol:chlorofom isoamyl alcohol extraction and 2 chloroform extractions. RNA was isopropanol precipitated, fractions were combined, and genomic DNA was depleted using Turbo DNase, followed by cleanup with RNAclean beads. Polysome-associated RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018 and Kiefer et al. Journal of the American Chemical Society 2018. To isolate RNA from stressed polysome fractions, each fraction was ethanol precipitated, resuspended and fractions were combined, and then samples were TRIzol extracted.  Genomic DNA was depleted using Turbo DNase, followed by cleanup with RNAclean beads. Total RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018 and Kiefer et al. Journal of the American Chemical Society 2018.
RNA sequencing libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413).

treatment_protocol: S2 cells were heat shocked at 37℃ for 1 hour minutes and 100uM s4U, 100uM s6G, or control water and DMSO for 45 minutes. 293T cells were treated with 500nM flavopiridol or DMSO control for 2 hour and 100uM s4U or 100uM s6G or water and DMSO control 2 hours. Or 293T cells were treated with 100uM s4U, 100uM s6G or water and DMSO control for 4 hours. Cell lysates were treated +/- 2mM puromycin on ice for 20 minutes, and then at 37℃ for 20 minutes.

tag: genotype

value: WT

tag: s4u feed

value: No

tag: s6g feed

value: Yes

tag: molecule subtype

value: total RNA


title: Donor2_4th-stimulated_PRDM1_2

city: Philadelphia

first: Inyoung

last: Jung

state: PA

address: SPE, 9-304, 3400 Civic Center Blvd, Bldg. 421

institute: University of Pennsylvania

data_processing:
Reads were pseudoaligned to the human genome (GRCh38) transcriptomes using kallisto v0.46.0. Differential expression analyses between AAVS1 KO PSMA CAR T-cells and PRDM1 KO PSMA CAR T-cells were performed using the edgeR v3.34.0 and limma v3.48.0 packages. Briefly, expression data were normalized using a trimmed mean of log expression ratios method and transformed into log2(counts per million). Linear models were used to assess differential expression, and P values were adjusted using the Benjamini and Hochberg method.
Supplementary files format and content: tsv files include TPM values for each Sample
Assembly: GRCh38

source_name: blood

growth_protocol: Healthy donor T-cells were isolated from peripheral blood mononuclear cells (PBMC) using the Pan T Cell Isolation Kit according to the manufacturer’s instructions (Miltenyi Biotec). T-cells were activated with anti-CD3/CD28 antibody coated Dynabeads (Thermo Fisher Scientific) at 3:1 bead:cell ratio in T-cell media (OpTmizer CTS SFM media (Gibco) supplemented with 5% human AB serum and 100u/mL human IL-2). Following a 24-hour incubation, lentivirus encoding the PSMA CAR was added to the culture at a multiplicity of infection (MOI) of 2.5.  Following T-cell activation, beads were removed using a magnet on day 3 and electroporation was carried out with a P3 primary cell 4D-nucleofector kit (Lonza). 2 × 106 CAR T-cells were transfected with 12 µg TrueCutTM S. pyogenes Cas9 (Invitrogen) and 0.2nmol of chemically-modified tracrRNA and crRNA (Integrated DNA Technologies).

extract_protocol: On days 0, 5 and 20 of the CAR T-cell restimulation assay, before stimulation and after the fourth tumor challenge respectively, CD8+ CAR T-cells were isolated using CD8 microbeads (Miltenyi Biotec) and total mRNA was extracted with RNA Clean & Concentrator™ kits (Zymo Research). Bulk RNA-seq was conducted by Novogene using the Novaseq6000 system (paired-end 150bp) at 40 × 106 reads per sample.

treatment_protocol: AAVS1 KO and PRDM1 KO PSMA CAR-positive T-cells were isolated using a Biotin-goat anti-mouse IgG F(ab)2 fragment (Jackson ImmunoResearch #115-065-072) and anti-biotin kits (Miltenyi Biotech). Following isolation, CAR T-cell purity was confirmed by flow cytometric analysis and CAR T-cells were then serially exposed (i.e., every 5 days) to irradiated PC3-PSMA cells at an effector-to-target (E:T) ratio of 3:1. Restimulation assays were followed up for 25-30 days since cell counts and viability become largely unreliable beyond 5-6th  round of stimulation due to senescent proliferative arrest and a marked decrease in the viability of chronically stimulated CAR T cells.

value: blood

tag: cell subtype

tag: cell type

value: T-cell

value: PRDM1 KO

tag: condition

tag: biological replicate

value: Normal donor 2_rep2


title: Methylation_450k_sample132

value: African American (AA)

tag: gender

value: F

tag: age(yrs)

tag: plate

tag: row

value: E


title: IP RNAPII Ctrl R1

description: Replicate 1

tag: cell line

tag: transfected sirna

value: Negative control siRNA anti-luciferase

tag: extract


title: TILAC_S2_s4UCntl

description:
Some processed data files for this sample contain no data because there were no reads in this sample with the corresponding number of mutations.
Reads filtered for number of T-to-C mutations (0-5+), G-to-A mutations (0-5+) and strandedness (min/pos)


title: P-6253_S-8498_ATAC

tag: tissue

tag: Sex

value: female

tag: age (years)

tag: location

value: brainstem

tag: diagnosis

value: high-grade glioma

tag: cellranger version(processing)

tag: technology

value: 10X Chromium Single Nuclei 3'


title: Methylation_450k_sample131

tag: race

value: M

tag: column

value: D

tag: pedigreeid

tag: subjectid

tag: phase


title: Donor1_4th-stimulated_PRDM1_2

tag: cell subtype

tag: cell type

tag: genotype

tag: condition

tag: biological replicate

value: Normal donor 1_rep2


title: Donor1_4th-stimulated_PRDM1_1

tag: tissue

value: Normal donor 1_rep1


title: TILAC_S2_HS_unlab

tag: cell line

value: WT

tag: s4u feed

value: No

tag: s6g feed

tag: molecule subtype

value: total RNA


title: Donor2_4th-stimulated_AAVS1_2

value: blood

value: T-cell

value: AAVS1 KO


title: Methylation_450k_sample128

value: African American (AA)

tag: gender

tag: age(yrs)

tag: plate

tag: row


title: Methylation_450k_sample129

tag: race

value: F

tag: column

value: C

tag: pedigreeid


title: Donor1_4th-stimulated_AAVS1_2

tag: cell subtype


title: Methylation_450k_sample130

tag: subjectid

tag: phase


title: TILAC_S2_s6GHS_s4UCntl_Rep1

tag: genotype

value: Yes


title: TILAC_S2_s6GHS_s4UCntl_Rep2


title: TILAC_S2_s4UHS_s6GCntl_Rep2


title: Methylation_450k_sample127

value: B


title: Donor2_4th-stimulated_PRDM1_1

tag: cell type

value: PRDM1 KO

tag: condition

tag: biological replicate

value: Normal donor 2_rep1


title: Methylation_450k_sample133


title: Donor1_4th-stimulated_AAVS1_1

tag: tissue


title: TILAC_S2_s4UHS

tag: cell line

tag: s4u feed

tag: s6g feed


title: Methylation_450k_sample126

tag: gender

tag: age(yrs)


title: Donor2_4th-stimulated_AAVS1_1


title: Methylation_450k_sample125

tag: plate

tag: row

value: A


title: TILAC_S2_s4UHS_s6GCntl_Rep1

tag: molecule subtype


title: Srf-KO, replicate 3

city: Uppsala

first: Michael

middle: Martin

last: Orlich

address: Dag Hammarskjölds Väg 20  Floor C11

department: Department of Immunology, Genetic and Pathology

country: Sweden

institute: Uppsala University

description: column name "PC_KO3"

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
TopHat2 (version 2.1.1) was used for alignment to the mouse genome assembly (GRCm38.p6 Ensembl release 92)
HTSeq-count (version 0.6.1) was used to generate gene expression count data with the option "-m intersection-nonempty"
DeSeq2 package was used for differential gene expression analysis across samples for protein-coding genes
Assembly: GRCm38.p6 Ensembl release 92
Supplementary files format and content: tab-delimited text files include FPKM values (abundance measurement) for each sample.

organism: Mus musculus

source_name: Retina

extract_protocol:
Eye balls from P12 pups were harvested and collected in ice cold MEM (Gibco, #31095-029) supplemented with 25 mM HEPES (Thermofisher, #15630049), penicillin/streptomycin (Gibco, #15140) and 10% fetal calf serum (FCS). Retinas were subsequently dissected and enzymatically digested using the Papain Dissociation Kit (Worthington Biochemical Corporation, #LK003150). After digestion, the single-cell suspension was filtered through a 40 µm cell strainer into a 2 ml reaction tube. Hereafter, the filtered cell suspension was centrifuged for 5 min at 300 x g at 4 °C and the supernatant was carefully removed. The remaining cell pellet was resuspended in 120 µl of FACS buffer (2% FCS and 2mM EDTA pH 8.0). 100 µl of the resuspended cells were mixed with 100 µl of FACS buffer containing fluorescently labeled ABs (Ter119-PB, CD45-PB, CD140a-FITC, CD140b-APC and CD31-PE, final dilutions see Online Table I), followed by incubation for 30 min on ice. The remaining 20 µl of whole retina single-cell suspension was kept as an input control and lysed in 350 µl of RLT buffer plus (Quiagen) supplemented with β-mercaptoethanol (10 µl/ml).  After AB incubation, 1 ml of FACS buffer was added to the cell suspension to wash out unbound ABs, followed by centrifugation for 5 min at 300 x g at 4 °C. Finally, the supernatant was carefully removed and the remaining cell pellet was resuspended in 500 µl FACS buffer containing 50 ng/ml DAPI (Sigma, #D9542) to label dead cells. Labeled single cell suspensions were sorted subsequently on a BD FACS Aria lllu sorter (BD Bioscience) using a 100 µm nozzle. Gating strategies for discrimination of cell populations were based on their immunolabelling defined according to reference experiments using single-stained samples and fluorescence minus one (FMO) controls.
160-590 pg of RNA were used for sequencing library preparation with the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England BioLabs). Libraries were validated in the 2100 BioAnalyzer and quantified by qPCR and fluorometric analysis (Qubit 2.0, Invitrogen).

treatment_protocol: Animals were treated with Tamoxifen (Sigma-Aldrich #T5648) from P1 to P3 (50 µg)

value: Retina

value: Mural cell

value: Srf fl/fl-PdgfrbCre (+/-)

tag: treatment

value: Tamoxifen P1-P3 (50 ug)


title: Srf-KO, replicate 2

description: column name "PC_KO2"


title: Donor2_Pre-stimulatde_PRDM1_1

tag: cell subtype

value: Pre-stimulated


title: Srf-KO, replicate 1

description: column name "PC_KO1"


title: TILAC_S2_Cntl_unlab

value: WT

value: No

value: total RNA


title: Donor2_Pre-stimulated_AAVS1_1

value: blood

value: T-cell

value: AAVS1 KO


title: Methylation_450k_sample124

tag: race

value: African American (AA)

value: F

tag: column

value: C

tag: pedigreeid

tag: subjectid


title: Methylation_450k_sample123

value: M

value: H

tag: phase


title: Srf-Ctrl, replicate 3

description: column name "PC_CTRL3"

tag: cell type

tag: genotype

value: Srf fl/fl-PdgfrbCre (-/-)


title: Donor1_Pre-stimulated_PRDM1_2

tag: tissue

value: PRDM1 KO

tag: condition

tag: biological replicate

value: Normal donor 1_rep2


title: Srf-Ctrl, replicate 2

description: column name "PC_CTRL2"

value: Retina

value: Mural cell


title: Methylation_450k_sample122

tag: gender

value: B


title: Donor2_Pre-stimulated_PRDM1_2

value: Pre-stimulated

value: Normal donor 2_rep2


title: Srf-Ctrl, replicate 1

description: column name "PC_CTRL1"

value: Tamoxifen P1-P3 (50 ug)


title: Methylation_450k_sample120

tag: age(yrs)

value: A


title: Methylation_450k_sample119

tag: plate


title: Donor1_Pre-stimulated_PRDM1_1

value: blood

value: T-cell

value: Normal donor 1_rep1


title: Methylation_450k_sample121

value: African American (AA)

tag: row

value: G


title: Donor1_Pre-stimulated_AAVS1_2

value: AAVS1 KO


title: Methylation_450k_sample118

value: F


title: Donor2_PRDM1_1

data_processing:
FASTQ files for each sample were trimmed of adapter contamination using cutadapt (https://github.com/marcelm/cutadapt/). They were aligned to the hg19 reference genome using Bowtie2, restricting to properly aligned and properly paired reads between 10 and 1000 base pairs. Mitochondrial reads were removed (https://github.com/jsh58/harvard/blob/master/removeChrom.py). Files were sorted using samtools, and PCR duplicates were removed using Picard. BAM files were indexed using samtools in order to visualize tracks in IGV. Peak calling was performed with MACS2 with an FDR q-value of 0.01. The R package Diffbind was used to remove ENCODE blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists), then to identify peaks differentially opened between the control and the PRDM1 knockout.
Supplementary files format and content: bigwig files
Assembly: hg19

extract_protocol: Nuclei were isolated from CD8+ T-cells for each replicate, followed by the transposition reaction in the presence of Tn5 transposase (Illumina, Inc.) for 45 minutes at 37°C. Purification of transposed DNA was then completed with the MinElute Kit (Qiagen) and fragments were barcoded with dual indexes (Illumina Nextra). Library preparation and sequencing were performed by Novogene using NovaSeq 6000 (paired-end 150bp reads) at a depth of 30 × 106 reads per sample.

treatment_protocol: Dead cells were eliminated using the Dead Cell Removal Kit (Miltenyi Biotec) and CD8+ CAR T-cells were isolated using CD8 microbeads (Miltenyi Biotec). 100,000 cells per sample were cryopreserved.

value: Normal donor 2_rep1


title: Methylation_450k_sample117


title: Donor2_PRDM1_2

value: PRDM1 KO


title: Donor2_Pre-stimulated_AAVS1_2


title: Donor2_AAVS1_2


title: Methylation_450k_sample116


title: Methylation_450k_sample115

value: M


title: Donor1_PRDM1_1


title: Donor2_AAVS1_1


title: Methylation_450k_sample114

value: H


title: Donor1_PRDM1_2

value: Normal donor 1_rep2


title: Methylation_450k_sample113

value: E


title: Methylation_450k_sample112


title: Donor1_AAVS1_1


title: Donor1_AAVS1_2


title: Methylation_450k_sample111

value: D


title: Methylation_450k_sample110


title: PC3-rep4

city: Foshan

first: Yong

last: Luo

state: Guangdong

address: 78 Weiguo Road

department: Department of Urology

country: China

institute: The Second People’s Hospital of Foshan, Affiliated Foshan Hospital of Southern Medical University

description: Gene expression of prostate cancer cell line

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to the GRCh38 genome assembly using Hisat2 version 2.1.0 with default parameters
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR function package in R program version 3.4.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: Prostate

growth_protocol: All cell lines were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum and antibiotics containing penicillin and streptomycin

extract_protocol:
The total RNA was isolated and obtained from all cell lines using TRIzol and chloroform.
Sequencing libraries were generated using NEBNest UltraTM RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: Prostate

tag: cell line

value: Prostate cancer cell line

value: WT


title: Methylation_450k_sample109

value: C


title: Donor1_Pre-stimulated_AAVS1_1

value: blood

value: T-cell

value: Pre-stimulated


title: PC3-rep3


title: PC3-rep2


title: Methylation_450k_sample108

value: African American (AA)


title: Methylation_450k_sample107


title: DU145-rep3


title: PC3-rep1


title: Methylation_450k_sample105


title: DU145-rep2


title: Methylation_450k_sample104


title: DU145-rep1


title: Methylation_450k_sample103

value: B


title: BPH-1-rep4

description: Gene expression of benign prostate cell line

value: Benign prostate cell line


title: Methylation_450k_sample102

value: F


title: BPH-1-rep1


title: BPH-1-rep3


title: Methylation_450k_sample100


title: Methylation_450k_sample99


title: BPH-1-rep2


title: Methylation_450k_sample106


title: Methylation_450k_sample98


title: DU145-rep4


title: Methylation_450k_sample94


title: Methylation_450k_sample96

value: A


title: Methylation_450k_sample97

value: G


title: Methylation_450k_sample95

value: M

value: H


title: VVova IgG

city: Pittsburgh

first: B. Rhodes

last: Ford

address: 4401 Penn Ave.

department: Department of Pediatrics

institute: University of Pittsburgh

description: CUT&RUN DNA

data_processing:
Library strategy: CUT&RUN
trimmed high quality reads were aligned to genome using bowtie2
bedgraph files were generated from alignment files using bedtools
BigWig files were generaed using bedGraphToBigWig
peaks were determined using MACS2 for peak calling, followed by idr
Differential peak analysis determined using DESeq2 on concatenated and merged peak files with cutoffs of 2 fold and p value<0.05
Genome_build: mm10_ensembl
Supplementary_files_format_and_content: BigWig

source_name: Spleen of VVova-infected mouse

growth_protocol: Mice were injected intradermally with 2.5 × 105 B16 melanoma cells. Mice were sacrificed and dLN and TIL harvested on day 14, when tumors were typically 8-10 mm in diameter.

extract_protocol:
CD8 T cells were isolated from tumors by surgical excision followed by flow sorting.CUT&RUN was performed as previously described (Skene et al., 2018). ).
Libraries were prepared using NEBNext Multiplex Oligos for Illumina and either the sparQ DNA Library Prep Kit ) or NEBNext Ultra II DNA Library Prep Kit for Illumina.  Cluster generation and 75-bp paired-end, dual-indexed sequencing were performed on the Illumina NextSeq 500 system.

tag: antibody

value: IgG

value: CD8+ T cell

tag: disease state

value: Vaccinia-Ova infection

tag: treatment

tag: timepoint

value: Day 8 post-infection

tag: sorting scheme


title: ASO-NT_rep3

city: South San Francisco

first: Amy

last: Easton

state: CA

address: 1 DNA Way

department: Department of Neuroscience

institute: Genentech, Inc

data_processing:
NovaSeq Control Software 1.7.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (0.32)
Basecalling was performed using Real-Time Analysis (RTA) v3.4.4 and fastq generated with bcl2fastq2.20 v2.20.0.422
Mapping of the reads was performed with STAR, followed by estimation of transcripts abundance using Biokit (Roche internal tool) and differential gene expression analysis performed with DESeq2
Assembly: GRCh38
Supplementary files format and content: pairwise analysis of ASO-001933- or ASO-NT-treated neuronal culture
Supplementary files format and content: tab-delimited text files include average reads per million, fold-changes, and adjusted pvalues

source_name: SA001 hESC

extract_protocol:
RNA isolation was performed using RNeasy Mini Kit  (Qiagen) following manufacture’s instruction.
RNA libraries for RNA-seq were prepared using TruSeq stranded total RNA library preparation protocol with RiboZero to remove rRNA (Illumina)
Coding and non-coding RNA-Seq

value: SA001 hESC

value: neuronal culture

value: wt

value: ASO-NT


title: ASO-001933 1uM_rep1


title: ASO-001933 1uM_rep2


title: ASO-NT_rep2


title: Methylation_450k_sample93

tag: race

tag: column

tag: pedigreeid

tag: subjectid


title: dLN IgG

description: CUT&RUN DNA

source_name: draining lymph node of B16 melanoma tumor

tag: cell type

value: B16 melanoma

value: Day 14 post-tumor


title: ASO-NT_rep1

tag: genotype


title: PD1hiTim3+ TIL Batf 1

description: CUT&RUN DNA

source_name: B16 melanoma tumor

tag: transcription factor

value: Batf


title: ASO-001933 1uM_rep3


title: Methylation_450k_sample92

value: African American (AA)

tag: gender

tag: phase


title: Methylation_450k_sample91

tag: age(yrs)

tag: plate

value: F


title: PD1hi TIL Batf 1

description: CUT&RUN DNA


title: glutamatergic neurons, ASO-001933 5uM rep3

data_processing:
NovaSeq Control Software 1.7.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (0.32)
Basecalling was performed using Real-Time Analysis (RTA) v3.4.4 and fastq generated with bcl2fastq2.20 v2.20.0.422
Mapping of the reads was performed with STAR (v2.5.1b), followed by estimation of transcripts abundance using RSEM (RNA-Seq by Expectation Maximization v1.3.0) and differential gene expression analysis performed with DESeq2 (v1.28.1 )
Assembly: GRCh38
Supplementary files format and content: pairwise analysis of ASO-treated and vehicle-treated Glutaneurons or Astrocytes
Supplementary files format and content: tab-delimited text files include average reads per million, fold-changes, and adjusted pvalues

source_name: iCell Glutaneurons

extract_protocol:
RNA isolation was performed using RNeasy Mini Kit  (Qiagen) following manufacture’s instruction.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Gold rRNA Removal Kit
Coding and non-coding RNA-Seq

tag: cell line

value: iCell Glutaneurons

value: neurons


title: glutamatergic neurons, ASO-001933 5uM rep1


title: glutamatergic neurons, ASO-001933 5uM rep2


title: Methylation_450k_sample90

tag: row


title: Methylation_450k_sample101

value: A


title: PD1lo TIL Batf 1

description: CUT&RUN DNA

tag: disease state


title: glutamatergic neurons, vehicle, rep2

tag: treatment

value: vehicle


title: dLN Batf 1

description: CUT&RUN DNA

tag: timepoint


title: Methylation_450k_sample89

value: E


title: glutamatergic neurons, vehicle, rep3


title: dLN Tox 2

description: CUT&RUN DNA

value: Tox

value: CD8+ T cell

tag: sorting scheme


title: Methylation_450k_sample88

tag: race

value: M

value: G


title: dLN Tox 1

description: CUT&RUN DNA


title: PD1hiTim3+ TIL Tox 2

description: CUT&RUN DNA


title: Methylation_450k_sample85

tag: column

value: C


title: exp_2_no_4sU

city: Cambridge

first: Jorge Diego

last: Martin Rufino

state: MA

address: 415 Main Street

institute: Harvard University / Broad Institute of MIT and Harvard / Boston Children's Hospital

description: scNT-seq

data_processing:
Sequencing files were demultiplexed using bcl2fastq v2.20 (Illumina). Fastq files from tagmentations belonging to the same time point were concatenated together. Using Dynast (https://github.com/aristoteleo/dynast-release), a wrapper around STARsolo (https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md), cell barcode and UMI sequencing errors were corrected and reads were aligned to the hg38v91 genome (16). Dynast count was used to parse the alignment BAM and quantify labeled/unlabelled/spliced/unspliced RNA and produce anndata h5ad files for each of the time points. We omitted background SNPs present in K562 by providing the genomic coordinates of SNPs computed on the non-chemically converted sample (which were defined as the genomic coordinates in which a mutation was present in >50% of reads).     To compute background mutation rates, we used two strategies: for the replicate with 0–6h chase time points, we used Dynast to compute the average mutation rate of non-T bases to any other base; for the replicate with 0–10h chase time points, we calculated the T-to-C mutation rate in a control sample treated with 4sU but without chemical conversion.
Assembly: hg38
Supplementary files format and content: anndata object (.h5ad)

source_name: Hematopoietic

growth_protocol: K562 erythroleukemia cells (ATCC, CCL-243) were cultured in RMPI 1640 + L-glutamine, with 10% FBS, 1% Penicillin / Streptomycin and 1% L-glutamine 200mM.

treatment_protocol: For 4-thiouridine (4sU) experiments, cells were plated in 6-well plates ~12h before the start the experiment at a density of 5x 10^5 – 8 x 10^5 cells/mL in 5mL of fresh media. 4sU (Sigma, T4509-25MG) in DMSO was added to culture wells at a final concentration of 100μM for 24h, with renewal every 6-8h. Between the pulse and chase phases, the cells were washed twice to remove any residual traces of 4sU. Subsequently, media with saturating concentrations of uridine (Sigma, U6381) at 10mM was added. Cells were collected at 0h, 2h, 4h, 6h, 8h, and 10h. All the samples from each pulse-chase experiment were processed the same day to minimize batch effects. To control for genes induced by the long exposure to 4sU and to uridine, two control samples with chase only or DMSO only were included.

tag: tissue

value: Hematopoietic

value: K562 (ATCC)

value: erythroleukemia


title: PD1hiTim3+ TIL Tox 1

description: CUT&RUN DNA

value: B16 melanoma

value: Day 14 post-tumor


title: PD1hi TIL Tox 2

description: CUT&RUN DNA


title: exp_2_no_4sU_8h_chase

description: scNT-seq


title: Methylation_450k_sample84

data_processing: For each chip, the Minfi R package was used to perform background correction and normalization. The regression on correlated probes (RCP) method was then used to adjust probe-type bias.

value: African American (AA)

tag: pedigreeid

tag: subjectid


title: PD1mid TIL Batf 1

description: CUT&RUN DNA

tag: antibody

value: Batf

tag: cell type


title: exp_2_NO_chemical_conversion

description: scNT-seq


title: Methylation_450k_sample82

tag: gender

value: F


title: Methylation_450k_sample83

value: D

tag: phase


title: PD1mid TIL Tox 2

description: CUT&RUN DNA

tag: transcription factor


title: exp_2_24h_4sU_10h_chase

description: scNT-seq

tag: time point


title: exp_2_24h_4sU_8h_chase

description: scNT-seq

tag: cell line


title: PD1hi TIL Tox 1

description: CUT&RUN DNA


title: PD1mid TIL Tox 1

description: CUT&RUN DNA


title: exp_2_24h_4sU_6h_chase

description: scNT-seq


title: Methylation_450k_sample81

tag: age(yrs)

tag: plate

tag: row


title: glutamatergic neurons, vehicle, rep1

value: iCell Glutaneurons

value: neurons

tag: genotype

value: wt

tag: treatment


title: PD1lo TIL Tox 2

description: CUT&RUN DNA

value: Tox

tag: disease state

tag: timepoint

tag: sorting scheme


title: Methylation_450k_sample80

tag: race

tag: column

value: E

tag: pedigreeid


title: Methylation_450k_sample87

tag: subjectid


title: PD1lo TIL Tox 1

description: CUT&RUN DNA

tag: cell type

value: CD8+ T cell


title: exp_2_24h_4sU_2h_chase

description: scNT-seq

tag: tissue


title: exp_2_24h_4sU_4h_chase

description: scNT-seq


title: Methylation_450k_sample86

tag: gender

tag: phase


title: Methylation_450k_sample79

value: B


title: dLN H3K9ac 2

description: CUT&RUN DNA

tag: antibody


title: exp_2_24h_4sU_0h_chase

description: scNT-seq

tag: cell line

tag: time point


title: Methylation_450k_sample77

tag: age(yrs)

tag: plate

tag: row

value: A


title: Methylation_450k_sample78

value: M


title: dLN H3K9ac 1

description: CUT&RUN DNA

tag: disease state

tag: treatment


title: PD1hiTim3+ TIL H3K9ac 2

description: CUT&RUN DNA

tag: timepoint

tag: sorting scheme


title: Methylation_450k_sample76

tag: race

tag: column

value: C


title: PD1hiTim3+ TIL H3K9ac 1

description: CUT&RUN DNA


title: Methylation_450k_sample75

value: H

tag: pedigreeid

tag: subjectid


title: exp_1_24h_4sU_1h_chase

description: scNT-seq

tag: tissue

value: Hematopoietic

value: K562 (ATCC)

tag: cell type

value: erythroleukemia


title: exp_1_24h_4sU_6h_chase

description: scNT-seq


title: exp_1_24h_4sU_2h_chase

description: scNT-seq


title: exp_1_24h_4sU_0h_chase

description: scNT-seq


title: PD1hi TIL H3K9ac 2

description: CUT&RUN DNA

value: B16 melanoma

value: Day 14 post-tumor


title: Methylation_450k_sample74

value: African American (AA)

tag: gender

value: F

tag: phase


title: PD1lo TIL H3K9ac 1

description: CUT&RUN DNA

tag: antibody


title: Methylation_450k_sample70


title: Topo1cc_Veh_LNCAP_exp2

source_name: LNCAP cells

tag: cell line

value: LNCAP

value: human prostate cancer cells

value: Vehicle

tag: chip antibody

value: TopoGEN TG2017-2 (Lot# 17AG15)


title: Methylation_450k_sample69

tag: age(yrs)

tag: plate

value: G


title: PD1hi TIL H3K9ac 1

description: CUT&RUN DNA

value: CD8+ T cell

tag: disease state


title: Topo1cc_Veh_LNCAP_exp1

tag: treatment


title: Topo1_Veh_exp3

value: human breast cancer cells


title: PD1mid TIL H3K9ac 1

description: CUT&RUN DNA

tag: timepoint


title: dLN H3K27ac 2

description: CUT&RUN DNA

tag: sorting scheme


title: Topo1_E2_14h_exp3


title: Topo1_E2_1h_exp3


title: PD1mid TIL H3K9ac 2

description: CUT&RUN DNA


title: PD1hiTim3+ TIL H3K27ac 2

description: CUT&RUN DNA


title: Methylation_450k_sample71

tag: race

value: M

tag: row


title: Methylation_450k_sample72

tag: column

value: A

tag: pedigreeid


title: PD1lo TIL H3K9ac 2

description: CUT&RUN DNA


title: Methylation_450k_sample66

value: H

tag: subjectid


title: Methylation_450k_sample68


title: Topo1cc_Veh_exp4

tag: cell type


title: Methylation_450k_sample67

tag: gender


title: Topo1cc_E2_14h_exp4


title: Methylation_450k_sample63

value: D

tag: phase


title: PD1hi TIL H3K27ac 1

description: CUT&RUN DNA

tag: antibody


title: dLN H3K27ac 1

description: CUT&RUN DNA


title: IgG_Veh_LNCAP

tag: cell line

value: Millipore PP64B (Lot#3229748)


title: Methylation_450k_sample65

value: E


title: Topo1cc_DHT_60min_LNCAP_exp1

tag: chip antibody


title: Ku70_Veh_LNCAP_exp2

value: Veh


title: Methylation_450k_sample61

tag: age(yrs)

value: C


title: PD1hi TIL H3K27ac 2

description: CUT&RUN DNA

value: B16 melanoma

value: Day 14 post-tumor


title: Methylation_450k_sample73

value: African American (AA)

value: F

tag: plate


title: PD1mid TIL H3K27ac 2

description: CUT&RUN DNA

tag: disease state


title: PD1hiTim3+ TIL H3K27ac 1

description: CUT&RUN DNA

tag: treatment


title: H3K27me3_Veh_LNCAP

value: LNCAP

value: human prostate cancer cells

value: Vehicle


title: Ku70_Veh_LNCAP_exp1


title: Methylation_450k_sample59


title: Methylation_450k_sample62


title: H3K27me3_Veh_exp3


title: Topo1cc_DHT_60min_LNCAP_exp2

value: TopoGEN TG2017-2 (Lot# 17AG15)


title: Methylation_450k_sample64

value: G


title: PD1lo TIL H3K27ac 1

description: CUT&RUN DNA

value: CD8+ T cell

tag: timepoint


title: Methylation_450k_sample60


title: PD1lo TIL H3K27ac 2

description: CUT&RUN DNA

tag: sorting scheme


title: OT-I from VVova Infection H3K27me3 2

description: CUT&RUN DNA

value: Vaccinia-Ova infection

value: Day 8 post-infection


title: Ku70_TNFa_1h_exp2

value: human breast cancer cells


title: PD1mid TIL H3K27ac 1

description: CUT&RUN DNA


title: Methylation_450k_sample56

tag: race

value: B


title: dLN H3K27me3 1

description: CUT&RUN DNA


title: Ku70_TNFa_14h_exp2


title: dLN H3K27me3 2

description: CUT&RUN DNA


title: IgG_Veh_exp4

value: Millipore PP64B (Lot#3229748)


title: Methylation_450k_sample58

tag: row


title: Methylation_450k_sample55

tag: column

value: D


title: Methylation_450k_sample54

value: M

value: A

tag: pedigreeid


title: OT-I from VVova Infection H3K27me3 1

description: CUT&RUN DNA


title: PD1hiTim3+ TIL H3K27me3 1

description: CUT&RUN DNA

value: B16 melanoma

value: Day 14 post-tumor


title: Ku70_DHT_60min_LNCAP_exp2


title: PD1hi TIL H3K27me3 2

description: CUT&RUN DNA


title: PD1hiTim3+ TIL H3K27me3 2

description: CUT&RUN DNA


title: Methylation_450k_sample53

value: African American (AA)

value: C

tag: subjectid


title: Ku70_DHT_60min_LNCAP_exp1

value: LNCAP

tag: cell type

value: human prostate cancer cells


title: HP1g_Veh_siNC_exp6


title: PD1mid TIL H3K27me3 2

description: CUT&RUN DNA


title: Methylation_450k_sample51

tag: gender

value: F


title: Methylation_450k_sample52

value: H

tag: phase


title: Ku70_Veh_exp2

value: Veh

tag: antibody


title: Methylation_450k_sample50

value: G


title: HP1g_Veh_siKu70_exp6

tag: cell line


title: Methylation_450k_sample57

value: E


title: HP1g_Veh_LNCAP_exp2


title: Methylation_450k_sample49


title: HP1g_Veh_LNCAP_exp1


title: Ku70_E2_14h_exp2

value: human breast cancer cells


title: Methylation_450k_sample47

value: B


title: Methylation_450k_sample48


title: PD1lo TIL H3K27me3 2

description: CUT&RUN DNA

value: CD8+ T cell


title: PD1lo TIL H3K27me3 1

description: CUT&RUN DNA


title: OT-I from VVova Infection H3K4me3 2

description: CUT&RUN DNA

value: Vaccinia-Ova infection

value: Day 8 post-infection


title: HP1g_TNFa_14h_exp4


title: HP1g_E2_1h_siNC_exp6


title: HP1g_TNFa_1h_exp4


title: PD1hi TIL H3K27me3 1

description: CUT&RUN DNA


title: OT-I from VVova Infection H3K4me3 1

description: CUT&RUN DNA


title: Methylation_450k_sample45

value: A


title: HP1g_Veh_exp4


title: PD1mid TIL H3K27me3 1

description: CUT&RUN DNA

value: B16 melanoma


title: dLN H3K4me3 1

description: CUT&RUN DNA

value: Day 14 post-tumor


title: dLN H3K4me3 2

description: CUT&RUN DNA


title: Methylation_450k_sample44

value: African American (AA)

value: M


title: HP1g_E2_1h_siKu70_exp6


title: Methylation_450k_sample43


title: PD1hiTim3+ TIL H3K4me3 2

description: CUT&RUN DNA


title: ChIP-seq_CBX3_siTop1_Veh_MCF7

data_processing:
Basecalls performed using CASAVA version 1.4
Seqencing reads were aligned to the hg38 genome assembly using Bowtie version 2.0.1.
Genome binding peaks were identified using the 'findPeaks' command in HOMER with setting of '-style factor': 200 bp peaks with 3-fold enrichment and 0.01 FDR significance over local tags.
To generate histograms for the average distribution of tag densities, position-corrected, normalized tags in 100 bp windows were tabulated within the indicated distance from specific sites in the genome. Clustering plots for normalized tag densities at each genomic region were generated using HOMER and then clustered using Gene Cluster 3.0.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: Human breast cancers

extract_protocol:
Briefly, cells were cross-linked with 1% formaldehyde at room temperature for 10 min. And then the cross-linking was quenched with 0.125M glycine for 5 min. Chromatin was fragmented using a Bioruptor® Pico (Diagenode) for 10 min at high power, with an interval of 30 s between pulses to get around 200bp fragments and precleared using 20 μl Protein G Dynabeads (Life Technologies, Cat# 10009D). Subsequently, the soluble chromatin was incubated with 2-5 μg antibodies at 4°C overnight. Immunoprecipitated complexes were collected using 30 μl Protein G Dynabeads, which have been saturated with PBS/1% BSA over night at 4°C, per reaction. For all ChIPs, after de-crosslinking overnight at 65°C, final ChIP DNA was extracted and purified using QIAquick spin columns (QIAGEN).
The libraries were constructed following Illumina’s Chip-Seq Sample prep kit.

treatment_protocol: For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM. TNFalpha (R&D systems) was added to a final concentration of 20 ng/ml. 5α-dihydrotestosterone (DHT, Sigma) was added to a final concentration of 100 nM. The ethanol (EtOH) vehicle control was 0.05% in all samples.

tag: chip antibody

value: CTCF Active Motif 61311(Lot#34614003)


title: PD1hiTim3+ TIL H3K4me3 1

description: CUT&RUN DNA


title: ChIP-seq_CBX3_siTop1_E2_MCF7


title: HP1g_E2_14h_exp4


title: Methylation_450k_sample46

source_name: peripheral blood leukocytes

extract_protocol: genomic DNA was extracted from stored peripheral blood leukocytes using AutoGen FlexStar (AutoGen, Holliston, MA) and DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA)

tag: age(yrs)


title: TILAC_S2_s6GHS

tag: genotype

value: WT

tag: s4u feed

value: No

tag: s6g feed

value: Yes

tag: molecule subtype

value: total RNA


title: ChIP-seq_CBX3_siNC_E2_MCF7

tag: treatment

value: Anti-HP1gamma clone 42s2 Millipore 05-690 (Lot#3224566)


title: ChIP-seq_CBX3_siNC_Veh_MCF7


title: HP1g_DHT_60min_LNCAP_exp2

value: LNCAP

value: human prostate cancer cells


title: Methylation_450k_sample41

tag: race

value: F

tag: plate

value: G


title: Methylation_450k_sample39

tag: column

tag: row


title: Methylation_450k_sample38

value: C

tag: pedigreeid

tag: subjectid


title: PD1mid TIL H3K4me3 1

description: CUT&RUN DNA

tag: cell type

value: CD8+ T cell

tag: disease state

tag: timepoint

tag: sorting scheme


title: PD1hi TIL H3K4me3 2

description: CUT&RUN DNA

tag: antibody


title: PLZ_Combo_S119

city: Minneapolis

first: Bayardo

middle: Isidore

last: Garay

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

description: day-30 hiPSC-CMs

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Tophat (v2.0.13) using the mouse (mm10 as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: hg38
Supplementary_files_format_and_content: BayardoRawReadCounts.txt

molecule: polyA RNA

source_name: MAPKi

growth_protocol: All three hiPSC lines were maintained in mTeSR™-1 medium (STEMCELL Technologies) on growth factor-reduced (GFR) Matrigel (~8μg/cm2, Corning) at 5% CO2 and 37°C under normoxia conditions. Cells were singularized with Accutase (Innovative Cell Technologies, Inc.) for 3-5 minutes and passaged every 4 days at a density of 1.25 × 104 /cm2 with the addition of 10μM ROCK inhibitor (Y-27632, Cayman Chemical) for the first 24 hours after each passage. Cell lines were routinely tested for mycoplasma contamination every 3 months (Applied Biological Materials, Inc.) following the manufacturer’s recommendation.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) and the PureLink RNA mini kit (Invitrogen, #12183025) with on-column DNase treatment following the manufacturer’s recommendations.
RNA libraries were prepared for sequencing using Illumina Truseq protocols

treatment_protocol: hiPSCs were cultured in 12-well plates to a confluency of 70-85% over 3 days in GFR-Matrigel (~22μg/cm2), and were induced with 6.5–8.5μM CHIR 99021 (GSK3β inhibitor, Cayman Chemical) in RPMI1640 (Gibco) supplemented with B27 (minus insulin, Gibco). Exactly 48 hours later, the media was completely removed and replaced with 7.5μM IWP-2 (PORCN inhibitor, Cayman Chemical) in RPMI1640 supplemented with B27 (minus insulin). Following another 48-hour period, the media was removed and replaced with RPMI1640 supplemented with B27 (minus insulin) on day 4 of the protocol. Beginning on day 6, the media was changed to RPMI1640 supplemented with B27 (plus insulin, Gibco) and changed every 48 hours. Beating was observed between day 8–12 of the differentiation protocol. hiPSC-CMs were purified using DL-lactate to induce a metabolic switch, as previously described26,29. Briefly, on day 15 of the differentiation protocol, hiPSC-CMs were incubated with 0.25% trypsin in EDTA for 20 minutes, singularized, and quenched with three times the volume of trypsin in filtered RPMI1640 with 20% FBS (Sigma-Aldrich). Cells were centrifuged at 300g for 5 minutes and resuspended in RPMI1640 supplemented with B27 (plus insulin) and 10μM ROCK inhibitor. hiPSC-CMs were then seeded onto two 6-well plates per every 12-well plate (~2.6x dilution by surface area). Forty-eight hours later, the media was changed to lactate media: RPMI1640 without D-glucose (Life Technologies), 5mM sodium DL-lactate (L4263, Sigma-Aldrich), 213μg/mL L-ascorbic acid 2-phosphate (Sigma-Aldrich), and 500μg/mL O. sativa-derived recombinant human albumin (Sigma-Aldrich). Media was changed every 48 hours for a total of 2 to 6 days upon which the media was reverted to RPMI1640 with B27 (plus insulin) supplement.

tag: cell line

value: PLZ


title: HP1g_DHT_60min_LNCAP_exp1


title: PLZ_DMSO_S116

description: day-30 hiPSC-CMs

source_name: DMSO


title: PD1lo TIL H3K4me3 1

description: CUT&RUN DNA

value: B16 melanoma


title: HP1g_E2_1h_exp4

source_name: MCF7 cells

value: human breast cancer cells


title: PD1mid TIL H3K4me3 2

description: CUT&RUN DNA

value: Day 14 post-tumor


title: PD1lo TIL H3K4me3 2

description: CUT&RUN DNA


title: Methylation_450k_sample40

value: African American (AA)

tag: gender

tag: age(yrs)

value: D

tag: phase


title: Methylation_450k_sample37

value: M

value: E


title: MYL2_Combo_S111

description: day-30 hiPSC-CMs


title: MYL2_DMSO_S108

description: day-30 hiPSC-CMs

value: DMSO


title: 19004_D86_2_S123

description: day-86 hiPSC-CMs

source_name: day-90 control

tag: ttreatment

value: day-90 control


title: MYL2_D86_S122

description: day-86 hiPSC-CMs

tag: treatment


title: 19004_DMSO_S112

description: day-30 hiPSC-CMs


title: 19004_D90_S120

description: day-90 hiPSC-CMs


title: Top1cc-seq_60min_CPT_LNCAP

data_processing:
Library strategy: TOP1cc-seq
Basecalls performed using CASAVA version 1.4
Seqencing reads were aligned to the hg38 genome assembly using Bowtie version 2.0.1.
Genome binding peaks were identified using the ‘findPeaks’ command in HOMER with setting of ‘-style factor’: 200 bp peaks with 3-fold enrichment and 0.01 FDR significance over local tags.
To generate histograms for the average distribution of tag densities, position-corrected, normalized tags in 100 bp windows were tabulated within the indicated distance from specific sites in the genome. Clustering plots for normalized tag densities at each genomic region were generated using HOMER and then clustered using Gene Cluster 3.0.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: Human prostate cancers

extract_protocol:
To perform TOP1cc-seq, approximately 2x10e6 cells were treated with 10 μM CPT (Selleckchem, Cat# S1288) for 10 mins and E2 or DHT, and then washed once with ice-cold 1x PBS with freshly added Proteinase inhibitors. The cells were directly in resuspended in Buffer A (50mM Tris-HCl, pH7.4, 1% SDS, 0.5% Empigen BB, 10 mM EDTA) with freshly added 1mM PMSF and Proteinase inhibitors at room temperature for 5 mins and incubate them in ice. Extracts were then sonicated using the Bioruptor® 300 (Diagenode) for 12 cycles [30 s “ON,” 30 s “OFF”] at high power setting for MCF7 cells, and 6 cycles [30 s “ON,” 30 s “OFF”] at high power setting for LNCAP cells. Cell lysate was centrifuged at 21,000 g for 10 min at 4°C and diluted with 9 times of Buffer B (20mM Tris-HCl, pH7.4, 100mM NaCl, 0.5% TritonX-100, 2mM EDTA) with freshly added Proteinase inhibitors. After pre-clear with 20 μl Protein G Dynabeads (Life Technologies, Cat# 10009D), 7 μg TOP1cc (TopoGEN, TG2017-2) was added and incubated with sample over night at 4°C for on a rotator. Immunoprecipitated complexes were collected using 30 μl Protein G Dynabeads, which have been saturated with PBS/1% BSA over night at 4°C, per reaction. And then the immunoprecipitated complexes were successively washed 2 times with pre-cold Washing Buffer I (10mM Tris-HCl, pH7.4, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.1% SDS, 1% TritonX-100, freshly added Proteinase inhibitors), 2 times with pre-cold Washing Buffer II (10mM Tris-HCl, pH7.4, 500mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 1% TritonX-100, freshly added Proteinase inhibitors), 1 time with pre-cold Washing Buffer III (10 mM Tris-HCl pH 7.4, 250 mM LiCl, 0.5% NP-40, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, freshly added Proteinase inhibitors) and 1 time with pre-cold TE buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA) with 100 mM NaCl and freshly added Proteinase inhibitors. All washes were performed at RT for 5 min on a rotator. SDS Elution Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) was added 1 μl RNase A (Thermo Scientific™, Cat# EN0531) and incubated at 37°C for 2 hr and then added 10 μl Proteinase K (Invitrogen™, Cat# AM2548) and incubated overnight to digest all the proteins. After overnight digestion, DNA was incubated with 5 times volume of PB buffer for 30 mins and purified using QIAquick PCR Purification Kit (QIAGEN, Cat# 28106) according to the manufacturer’s instructions.
The libraries were constructed following Illumina’s Chip-Seq Sample prep kit.

tag: ip antibody

value: TOP1cc (TopoGEN, catalog# TG2017-2, lot# 17AG15)


title: PD1hi TIL H3K4me3 1

description: CUT&RUN DNA


title: Methylation_450k_sample36

tag: race

tag: plate


title: Methylation_450k_sample33

tag: column

tag: row


title: Methylation_450k_sample32

value: B

tag: pedigreeid

tag: subjectid


title: 19004_D86_1_S121

description: day-86 hiPSC-CMs

tag: t treatment


title: PD1hiTim3+ TIL PD1 RNAseq 2

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_PD1_rep2

data_processing:
trimmed high quality reads were aligned to genome using HISAT2
Transcripts per Million (TPMs) calculated using Subread
Differentially expressed genes (DEG) determined using DEseq2 with cutoffs of 2 fold and padj<0.05
Genome_build: mm10 ensembl
Supplementary_files_format_and_content: Transcripts per Million (TPM) file, normalized counts

extract_protocol:
CD8 T cells were isolated from tumors by surgical excision followed by flow sorting. cDNA was prepared from ~1,000 cells using the SMART-seq v4 Ultra Low Input RNA Kit for Sequencing
Libraries were prepared using the Nextera XT DNA Library Preparation kit. Libraries were denatured and diluted using the NextSeq 500 protocol Revision D.Cluster generation and 75-bp paired-end, dual-indexed sequencing were performed on the Illumina NextSeq 500.

treatment_protocol: In immunotherapy experiments, when tumors were palpable (typically day 5), mice began anti-PD-1, anti-4-1BB, or isotype control therapy. Mice were treated with 200 μg of anti-PD-1, 200 μg of anti-4-1BB, or equivalent isotype control intraperitoneally three times per week for the duration of the experiment.

tag: cell type

tag: disease state

value: Anti-PD1 Antibody

tag: timepoint


title: PD1hiTim3+ TIL PD1 RNAseq 5

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_PD1_rep5

tag: sorting scheme


title: Methylation_450k_sample30

tag: gender

value: A


title: PD1hiTim3+ TIL PD1 RNAseq 4

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_PD1_rep4


title: 19004_Combo_S115

description: day-30 hiPSC-CMs

tag: cell line


title: Methylation_450k_sample31

tag: age(yrs)

tag: phase


title: PD1hiTim3+ TIL PD1 RNAseq 3

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_PD1_rep3

tag: treatment


title: Methylation_450k_sample34

value: F


title: PD1hiTim3+ TIL PD1 RNAseq 1

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_PD1_rep1


title: PD1hiTim3+ TIL 41BB RNAseq 6

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_41BB_rep6

value: Anti-41BB Antibody


title: Methylation_450k_sample35


title: Methylation_450k_sample29

value: C


title: PD1hiTim3+ TIL 41BB RNAseq 5

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_41BB_rep5

value: CD8+ T cell


title: Top1cc-seq_E2_30min_CPT_10min_MCF7_exp1

tag: ip antibody


title: PD1hiTim3+ TIL 41BB RNAseq 4

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_41BB_rep4

value: B16 melanoma


title: Methylation_450k_sample28

tag: race

value: H


title: Top1cc-seq_E2_10min_CPT_10min_MCF7_exp2


title: Top1cc-seq_E2_14h_CPT_10min_MCF7_exp1


title: mix of hiPSC and day4 hPGCLC [BTAG+]

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: Illumina Novaseq 6000 and Novaseq, S1 flowcell (100cycles), v1

data_processing:
Raw data were demultiplexed with the mkfastq command in Cell Ranger (v3.1.0) with default setting to generate fastq files. The fastq files were processed with count command in Cell Ranger with default setting to map to the reference genome for human GRCh38.p12 (hard masked PAR of chrY).
Genome_build: GRCh38.p12 (hard masked PAR of chrY)
Supplementary_files_format_and_content: Cell Ranger output, TSV and matrix files

source_name: hiPS and d4 BTAG+

extract_protocol:
For the sample collection from iPSCs and iMeLCs, the suspension of cells were generated as the same manner with passage or the induction of differentiation. For the aggregates of PGCLC induction at day1, the aggregates were collected, washed once in PBS, and dissociated with 0.25% Trypsin–EDTA for 10–15 min at 37°C with gentle pipetting every 5 min. Trypsin was neutralized with a 5× volume of 10% FBS in DMEM and washed once with 0.1% BSA in PBS.  Prior to proceeding the scRNA-seq analysis, the live single cells were sorted using FACS Aria III system (BD Biosciences) by FSC-SSC and DRAQ7 (ab109202) staining.
For the aggregates of PGCLC induction at day2 and day4, the aggregates were collected on the designated days of induction, washed once in PBS, and dissociated with 0.25% Trypsin–EDTA for 10–15 min at 37°C with gentle pipetting every 5 min. Trypsin was neutralized with a 5× volume of 10% FBS in DMEM and washed once with 0.1% BSA in PBS .  Prior to proceeding the scRNA-seq analysis, the live BTAG double positive single cells were sorted using FACS Aria III system (BD Biosciences) by FSC-SSC and EGFP-tdTomato gating with DRAQ7 (ab109202) staining. あんｄ
In case of iPSC and day4 BTAG double positive cells, the equal number of cells were mixed prior to the scRNA-seq analysis.
The cDNA library for NGS was conducted with Chromium Next GEM Single Cell 3' Kit v3.1 (Single Index) according to the manufacturer’s instructions.

tag: source cell type

value: human primodial germ cell like cell (PGCLC)

tag: cell culture protocol

value: hiPSCs were maintained under a feeder-free condition [StemFitTM (Ajinomoto, Tokyo, Japan) medium on recombinant LAMININ511 (rLN511E8) (iMatrix-511, Nippi, Tokyo, Japan)-coated cell culture plates] (Nakagawa et al., 2014). The hPGCLCs were induced by plating 5.0 × 10^3 iMeLCs into a well of a low-cell-binding V-bottom 96-well plate (greiner, 651970) in GK15 supplemented with 200 ng/ml of BMP4, 100 ng/ml of SCF (R&D Systems, 455-MC), 50 ng/ml of EGF (R&D Systems, 236-EG), 1000 U/ml of LIF (Millipore, #LIF1005) and 10 µM of the ROCK inhibitor.


title: TILAC_293T_s6GStress_s4UCntl_Ribo

source_name: Human embryonic kidney 293T cells

tag: genotype

value: WT

tag: s4u feed

value: Yes

tag: s6g feed

tag: molecule subtype

value: polysome-associated RNA


title: Top1cc-seq_E2_10min_CPT_10min_MCF7_exp1


title: Methylation_450k_sample27

value: African American (AA)

value: M

tag: plate

tag: column

tag: row

tag: pedigreeid

tag: subjectid


title: Methylation_450k_sample25

tag: gender


title: TILAC_293T_s4UStress_s6GCntl_Ribo

tag: cell line


title: Methylation_450k_sample24

tag: age(yrs)

tag: phase


title: PD1hiTim3+ TIL 41BB RNAseq 3

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_41BB_rep3

tag: cell type

tag: disease state

tag: treatment

tag: timepoint

value: Day 14 post-tumor

tag: sorting scheme


title: PD1hiTim3+ TIL IgG Control RNAseq 5

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_IgG_rep5

value: IgG Antibody


title: Methylation_450k_sample42

tag: race

value: E


title: Top1cc-seq_E2_30min_CPT_10min_MCF7_exp2

tag: ip antibody

value: TOP1cc (TopoGEN, catalog# TG2017-2, lot# 17AG15)


title: Methylation_450k_sample26

value: G


title: PD1hiTim3+ TIL 41BB RNAseq 1

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_41BB_rep1

value: Anti-41BB Antibody


title: PD1hiTim3+ TIL 41BB RNAseq 2

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_41BB_rep2


title: Top1cc-seq_E2_0min_CPT_10min_MCF7_exp1


title: TILAC_293T_s6GStress_s4UCntl_Input

description: Reads filtered for number of T-to-C mutations (0-5+), G-to-A mutations (0-5+) and strandedness (min/pos)

tag: genotype

tag: s4u feed

tag: s6g feed

tag: molecule subtype

value: total RNA


title: TILAC_293T_s6GStressNT_s4UStressPuro


title: PD1hiTim3+ TIL IgG Control RNAseq 4

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_IgG_rep4

value: CD8+ T cell


title: TILAC_293T_s4UStressNT_s6GStressPuro


title: Methylation_450k_sample22

value: F

tag: plate

tag: column

tag: row

tag: pedigreeid


title: Methylation_450k_sample20

tag: gender

tag: age(yrs)

tag: subjectid


title: PD1hiTim3+ TIL IgG Control RNAseq 2

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_IgG_rep2

tag: cell type

tag: disease state

value: B16 melanoma


title: TILAC_293T_s4UStress_s6GCntl_Input

tag: cell line


title: PD1hiTim3+ TIL IgG Control RNAseq 3

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_IgG_rep3

tag: treatment

tag: timepoint

tag: sorting scheme


title: TILAC_293T_Unfed_Puro

tag: genotype

value: No


title: Methylation_450k_sample23

tag: race

value: B

tag: phase


title: Methylation_450k_sample21

value: A


title: PRO-seq_siNC_Veh_1h_exp1

data_processing:
Library strategy: PRO-seq
Basecalls performed using CASAVA version 1.4
The sequencing reads were aligned to hg38 using Bowtie2 using very sensitive parameters.
The common artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data.
To determine E2-dependent changes in gene body, the sequencing reads for RefSeq genes were counted over the first 13 kb of the entire gene body, excluding the 500 bp promoter-proximal region on the sense strand with respect to the gene orientation by using HOMER. EdgeR21 was used to compute the significance of the differential gene expression (FC ≥ 1.5, FDR ≤ 0.01).
PRO-seqs were normalized to 10 million tags, and HOMER was used to quantify eRNA expression by tabulating normalized tag numbers surrounding ± 1,000 bp from the center of the peaks. eRNAs with a >1.5-fold change in GRO-seq or PRO-seq signals were considered to be differentially expressed.
Supplementary_files_format_and_content: bigWig

growth_protocol: MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen). For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM.

extract_protocol:
The resultant nuclei were washed two more times with 10ml lysis buffer and finally resuspended in 100 μl of freezing buffer (50mM Tris-HCl pH8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA).
For the run-on assay, resuspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-HCl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of SUPERase-In, 1% sarkosyl, 250 μM A/GTP, 50 µM biotin-11-C/UTP (Perkin-Elmer) and incubated for 5 min at 30°C. The resultant nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol® LS reagent (Life Technologies, Cat# 10296-028) following manufacturer’s instructions. NRO-RNA was fragmented to ∼200-500nt by alkaline base hydrolysis on ice for 30 min and and neutralized by adding 1× volume of 1 M Tris-HCl pH 6.8, Excessive salt and residual NTPs were removed by using P-30 column (Bio-Rad, Cat# 732-6250), followed by treatment with DNase I (Promega Cat# M6101) and antarctic phosphatase (NEB Cat# M0289L). Fragmented nascent RNA was bound to 10 µl of MyOne Streptavidin C1 dynabeads (Invitrogen, Cat# 65001) following the manufacturer’s instructions. The beads were washed twice in high salt (2 M NaCl, 50 mM Tris-HCl pH 7.5, 0.5% Triton X-100, 0.5 mM EDTA), once in medium salt (1M NaCl, 5 mM Tris-HCl pH 7.5, 0.1% Triton X-100, 0.5 mM EDTA), and once in low salt (5 mM Tris-HCl pH 7.5, 0.1% Triton X-100).
Bound RNA was extracted from the bead using Trizol (Invitrogen, Cat# 15596-018) in two consecutive extractions, and the RNA fractions were pooled, followed by ethanol precipitation and PRO-seq libraries were prepared with NEBNext® Small RNA Library Prep kit (NEB, Cat# E7330).

treatment_protocol: Briefly, ∼2 millions of MCF7 cells treated with E2 for 1 hr were washed 3 times with cold PBS and then sequentially swelled in swelling buffer (10mM Tris-HCl pH7.5, 2mM MgCl2, 3mM CaCl2) for 10 min on ice, harvested, and lysed in lysis buffer (swelling buffer plus 0.5% NP-40, 20 units of SUPERase-In, and 10% glycerol).

tag: agent

value: vehicle

tag: sirna

value: siNC


title: PRO-seq_siTop1_E2_1h_exp2


title: PRO-seq_siTop1_Veh_1h_exp1


title: Top1cc-seq_E2_0min_CPT_10min_MCF7_exp2

tag: ip antibody


title: PRO-seq_siTop1_E2_1h_exp1


title: PD1hiTim3+ TIL IgG Control RNAseq 1

description:
TPM_41BB_PD1TreatmentVsCtrl.csv
TIL_PD1hiTim3_IgG_rep1


title: PRO-seq_siNC_Veh_1h_exp2


title: OT-I from VVova Infection RNAseq 2

description:
TPM_TIL_LN_VVova.csv
VVova_rep2

value: Vaccinia-Ova infection

value: Day 8 post-infection


title: TILAC_293T_s6GNT_s4UPuro_Rep2

value: WT

tag: s4u feed

value: Yes

tag: s6g feed

tag: molecule subtype

value: polysome-associated RNA


title: Methylation_450k_sample18

value: African American (AA)

tag: gender

tag: age(yrs)

tag: plate

tag: column

tag: row

value: E

tag: pedigreeid


title: TILAC_293T_Unfed_NT

tag: cell line


title: PRO-seq_siTop1_Veh_1h_exp2


title: OT-I from VVova Infection RNAseq 3

description:
TPM_TIL_LN_VVova.csv
VVova_rep3

tag: cell type

tag: disease state

tag: treatment

tag: timepoint

tag: sorting scheme


title: OT-I from VVova Infection RNAseq 1

description:
TPM_TIL_LN_VVova.csv
VVova_rep1


title: PRO-seq_siNC_E2_1h_exp2

tag: agent

tag: sirna


title: Methylation_450k_sample17

tag: race

value: G

tag: subjectid

tag: phase


title: TILAC_293T_s4UNT_s6GPuro_Rep2

tag: genotype

tag: s4u feed

tag: s6g feed

tag: molecule subtype


title: dLN RNAseq 3

description:
TPM_TIL_LN_VVova.csv
LN_rep3

value: Day 14 post-tumor


title: Methylation_450k_sample19

tag: gender

value: M

tag: age(yrs)

tag: plate

tag: column

tag: row

value: H


title: TILAC_293T_s6GNT_s4UPuro_Rep1

tag: cell line


title: PRO-seq_siNC_E2_1h_exp1


title: Methylation_450k_sample16

value: F

value: D

tag: pedigreeid


title: TILAC_293t_500nMFP_unlabeledCntl

value: No

value: total RNA


title: Methylation_450k_sample15


title: TILAC_293t_500nMFP_unlabeledFP


title: dLN RNAseq 1

description:
TPM_TIL_LN_VVova.csv
LN_rep1

tag: cell type

value: CD8+ T cell

tag: disease state

value: B16 melanoma

tag: treatment

tag: timepoint

tag: sorting scheme


title: dLN RNAseq 2

description:
TPM_TIL_LN_VVova.csv
LN_rep2


title: RiboMinus replicate 2

city: Warsaw

first: Maria

middle: W

last: Górna

address: Żwirki i Wigury 101

department: Department of Chemistry

country: Poland

institute: Biological and Chemical Research Centre, University of Warsaw

description:
RiboMinus_2
counts_RAW.tsv
counts_TPM_normalized.tsv
countsProteinCoding_TPM_normalized.tsv
counts_medianOfRatiosNormalized.tsv
countsProteinCoding_medianOfRatiosNormalized.tsv
DifferentialExpression_RiboMinus_vs_Cin-S.tsv
DifferentialExpression_RiboMinus_vs_Con-B.tsv

data_processing:
The quality of the data received from the sequencing was checked with FastQC v0.11.9 software.
Reads were trimmed and filtered to remove contaminations and low quality reads with Trim Galore v0.6.7 (--quality 20, default auto-detection of adapters).
The high-quality filtered paired-end reads were aligned to Saccharomyces cerevisiae rRNA with bowtie2 v2.4.4, then resulting sequences were counted and removed from further analysis.
All remaining reads were aligned to the genome of Saccharomyces cerevisiae (NCBI: GCF_000146045.2_R64) using STAR v2.7.9a, allowing up to 4% of mismatches per read length. The resulting BAM files were used in the IGV v2.11.4 program to generate coverage plots of genes.
In the next step, all uniquely mapped reads were counted using featureCounts v2.0.3 and normalized to TPM (transcript per million) either for all reads or for reads mapping to coding sequences only, using a custom R script. Using TPM data, we generated bar charts and heatmap of expression for selected genes. Based on the annotations from the NCBI database and including previously deleted rRNA sequences, the percentages of individual RNA biotypes for all experimental groups were calculated.
The raw counts without non-coding sequences were loaded to the DEBrowser v1.22.2 web tool and genes with a maximum number of raw reads of 10 or less in all samples were filtered out. For PCA and volcano plots of differential expressed genes, the data was normalized with MRN. Differential expression analysis was performed using the DESeq2 v1.34.0 library.
Assembly: Saccharomyces cerevisiae RefSeq:GCA_000146045.2 R64
Supplementary files format and content: tab-delimited text files include RAW, TPM normalized and MRN normalized values for each Sample
Supplementary files format and content: tab-delimited text files include differential expression analysis using DESeq2 v1.34.0 library between treatment groups.

organism: Saccharomyces cerevisiae

extract_protocol:
RNA was extracted from the Saccharomyces cerevisiae strain BY4741, using a published protocol (Schmitt, Mark E., Timothy A. Brown, and Bernard L. Trumpower. "A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae." Nucleic acids research 18.10 (1990): 3091.) with modifications. 35 ml yeast cultures were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) to an OD600 of 0.6. The cells were harvested by centrifugation and the pellet was resuspended in 500 μl of AE Buffer (50 mM NaOAc pH 5.3, 10 mM EDTA), supplemented with 10% SDS. The suspension was vortexed with an equal volume of fresh phenol, previously equilibrated with an AE buffer. The mixture was incubated at 65°C for 5 min, rapidly chilled in liquid nitrogen, thawed at room temperature and centrifuged for 20 min at maximum speed to separate the aqueous and phenol phases. The aqueous phase was extracted twice with an equal volume of phenol/chloroform and once with 1/2 vol. of chloroform. RNA was precipitated from an aqueous phase by adding 1/10 vol. of 3 M NaOAc pH 5.3 and 2.5 vol. of ethanol, washed twice with 1 ml of ice cold 75-80% ethanol. RNA was submitted to treatment with TURBO DNase (Thermo Fisher Scientific) and RNA clean-up (with RNeasy Mini Kit, Qiagen) according to the manufacturer’s protocols. RNA was aliquoted and stored at -80°C.
In the Con-B method, a 50 μl portion of the Ni2+-Sepharose 6 Fast Flow (GE Healthcare) slurry beads was washed with RNase-free water and equilibrated in a chilled Binding Buffer (50 mM Tris pH 7.5, 150 mM NaCl, 1 mM DTT, 5 mM imidazole, 0.01% Tween 20, 3 mM MgCl2). Beads were sedimented by centrifugation at 500 ×g for 1 min at 4°C and the supernatant was discarded. A portion of 2-3 μg (35-55 picomole) of 6xHis-IFIT1 was immobilized on the beads under rolling mixing for 0.5-1 h at 4°C. The beads were sedimented as before and washed with 1 ml of the Binding Buffer. The binding of IFIT1 with RNA (a mixture of 4 of the in vitro transcribed RNAs or 10 μg of the total yeast RNA) was performed in 1 ml of Binding Buffer supplemented with Poly(dI-dC) (Poly(deoxyinosinic-deoxycytidylic acid) sodium salt, Sigma-Aldrich) at a final working concentration of 2 μg/ml, under rolling mixing for 1 h at 4°C. Prior to the capture procedure, RNA samples were heat denatured at 65-70°C for 10 min and placed on ice for 5 min before the binding. In the Cin-S method, IFIT1 was bound with RNA in 1 ml of the Binding Buffer supplemented with Poly(dI-dC) under rolling mixing for 1 h at 4°C and after that, the mixture was transferred to the pre-equilibrated beads for IFIT1-RNA complex immobilization. After binding, the beads were sedimented as before and washed several times with 1 ml of chilled Wash Buffer (50 mM Tris pH 7.5, 250 mM NaCl, 1 mM DTT, 5 mM imidazole, 0.01% Tween 20, 3 mM MgCl2). Selected RNA was released by proteolysis with Proteinase K (Invitrogen) for 1 h at 37°C. The eluted RNA was precipitated with ethanol, re-suspended in RNase-free water and used for further reactions. RNeasy Mini Kit (Qiagen) was used for RNA clean-up prior to RNA-seq. Depletion of rRNA with a commercial RiboMinus Transcriptome Isolation Kit (RiboMinus), yeast (Invitrogen) was performed according to the manufacturer’s protocol.
The strand-specific cDNA library was prepared using an Illumina Tru-Seq kit by the Genomics Core Facility, Centre of New Technologies, University of Warsaw. Sequencing was performed using Genome Sequencer Illumina NovaSeq 6000 PE100.

treatment_protocol: Two alternative pull-down protocols were used, Con-B (RNA-IFIT1 “complex on beads”) and Cin-S (RNA-IFIT1 “complex in solution”). Depletion of rRNA with a commercial RiboMinus Transcriptome Isolation Kit (RiboMinus), yeast (Invitrogen) was performed according to the manufacturer’s protocol.

value: Ribo Minus


title: RiboMinus replicate 3

description:
RiboMinus_3
counts_RAW.tsv
counts_TPM_normalized.tsv
countsProteinCoding_TPM_normalized.tsv
counts_medianOfRatiosNormalized.tsv
countsProteinCoding_medianOfRatiosNormalized.tsv
DifferentialExpression_RiboMinus_vs_Cin-S.tsv
DifferentialExpression_RiboMinus_vs_Con-B.tsv

growth_protocol: 35 ml yeast cultures were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) to an OD600 of 0.6


title: RiboMinus replicate 1

description:
RiboMinus_1
counts_RAW.tsv
counts_TPM_normalized.tsv
countsProteinCoding_TPM_normalized.tsv
counts_medianOfRatiosNormalized.tsv
countsProteinCoding_medianOfRatiosNormalized.tsv
DifferentialExpression_RiboMinus_vs_Cin-S.tsv
DifferentialExpression_RiboMinus_vs_Con-B.tsv


title: Con-B replicate 3

description:
Con-B_3
counts_RAW.tsv
counts_TPM_normalized.tsv
countsProteinCoding_TPM_normalized.tsv
counts_medianOfRatiosNormalized.tsv
countsProteinCoding_medianOfRatiosNormalized.tsv
DifferentialExpression_Cin-S_vs_Con-B.tsv
DifferentialExpression_RiboMinus_vs_Con-B.tsv

value: Con-B pull-down


title: Methylation_450k_sample13

tag: race

tag: subjectid

tag: phase


title: TILAC_293t_500nMFP_s6GCntl

data_processing:
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
Reads were aligned to the GRCh38 genome or dm6 genome using HISAT2 aligned with default parameters and --mp 4,2 .
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C and G-to-A mutations were identified using Rsamtools and a custom R script (available upon request). Only mutations at positions with a base quality score of greater than 45 that were at least three nt from the end of the read were counted.
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C and G-to-A SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C or G-to-A mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C or G-to-A mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph).
Tracks were converted to binary format using IGVtools (toTDF).
Genome_build: GRCh38 or dm6
Supplementary_files_format_and_content: TDF

tag: genotype

value: WT

tag: s4u feed

tag: s6g feed


title: Methylation_450k_sample14

tag: gender

tag: age(yrs)

value: C


title: Methylation_450k_sample12

tag: plate

tag: column


title: Methylation_450k_sample10

tag: row


title: TILAC_293T_s4UNT_s6GPuro_Rep1

tag: cell line

value: Yes

tag: molecule subtype

value: polysome-associated RNA


title: Con-B replicate 2

description:
Con-B_2
counts_RAW.tsv
counts_TPM_normalized.tsv
countsProteinCoding_TPM_normalized.tsv
counts_medianOfRatiosNormalized.tsv
countsProteinCoding_medianOfRatiosNormalized.tsv
DifferentialExpression_Cin-S_vs_Con-B.tsv
DifferentialExpression_RiboMinus_vs_Con-B.tsv


title: TILAC_293t_500nMFP_s4UFP_s6GCntl_Rep2


title: PD1hi TIL RNAseq 3

description:
TPM_TIL_LN_VVova.csv
TIL_PD1hi_rep3

tag: cell type

tag: disease state


title: TILAC_293t_500nMFP_s6GFP


title: TILAC_293t_500nMFP_s6GFP_s4UCntl_Rep2


title: Con-B replicate 1

description:
Con-B_1
counts_RAW.tsv
counts_TPM_normalized.tsv
countsProteinCoding_TPM_normalized.tsv
counts_medianOfRatiosNormalized.tsv
countsProteinCoding_medianOfRatiosNormalized.tsv
DifferentialExpression_Cin-S_vs_Con-B.tsv
DifferentialExpression_RiboMinus_vs_Con-B.tsv

tag: treatment


title: Methylation_450k_sample9

value: African American (AA)

value: E

tag: pedigreeid


title: TILAC_293t_500nMFP_s4UCntl


title: Cin-S replicate 3

description:
Cin-S_3
counts_RAW.tsv
counts_TPM_normalized.tsv
countsProteinCoding_TPM_normalized.tsv
counts_medianOfRatiosNormalized.tsv
countsProteinCoding_medianOfRatiosNormalized.tsv
DifferentialExpression_Cin-S_vs_Con-B.tsv
DifferentialExpression_RiboMinus_vs_Cin-S.tsv

value: Cin-S pull-down


title: Methylation_450k_sample8

tag: race

value: M

value: B


title: PD1hi TIL RNAseq 2

description:
TPM_TIL_LN_VVova.csv
TIL_PD1hi_rep2

tag: timepoint

value: Day 14 post-tumor

tag: sorting scheme


title: PD1hi TIL RNAseq 1

description:
TPM_TIL_LN_VVova.csv
TIL_PD1hi_rep1


title: Cin-S replicate 2

description:
Cin-S_2
counts_RAW.tsv
counts_TPM_normalized.tsv
countsProteinCoding_TPM_normalized.tsv
counts_medianOfRatiosNormalized.tsv
countsProteinCoding_medianOfRatiosNormalized.tsv
DifferentialExpression_Cin-S_vs_Con-B.tsv
DifferentialExpression_RiboMinus_vs_Cin-S.tsv

tag: genotype