title: 11_3E_UcNK_A164_F8_S164 : SS2 sample


title: 11_1i_UtrNK_A357_F9_S357 : SS2 sample

status: Public on May 20 2022

type: SRA

city: Oxford

first: Gurman

last: Kaur

address: Headley Way

department: John Radcliffe Hospital

country: United Kingdom

institute: University of Oxford

description: SmartSeq2 data for each individual cell with the listed Sample ID

library_source: transcriptomic single cell

data_processing:
RNA-Seq: bcl2fastq v.2.17.1.14, RSEM v.1.2.8
scRNA-Seq: CellRanger v2.1.0 (mkref and mkfastq), CellRanger v2.0.1 (count)
Supplementary files format and content: H5, .csv, .tsv

molecule: total RNA

organism: Mus musculus

source_name: mouse maternal-fetal interface

extract_protocol:
Isolation of cells from the implantation sites were done with enzymatic digestion using Liberase. For SMART-Seq2 processing, single cells were FACS sorted into 96 U-well plates into either trNK (NCR1+CD3ε-TCRb-CD19-CD45+CD122+CD49a+) or cNK (NCR1+CD3ε-TCRb-CD19-CD45+CD122+CD49b+) cells. For droplet-based scRNA-seq, total uNK cells (NCR1+CD3ε-TCRb-CD19-CD45+CD122+) were sorted into Eppendorf tubes.
RNA-Seq: SMART-Seq2 scRNA-seq libraries were prepared from trNK and cNK cells from gd9.5 maternal-fetal interface and sorted in 96 U-well plates. Libraries were prepared using Nextera XT DNA library preparation kit and sequenced using a NextSeq 500/550 High Output v2 kit 75 cycles (Illumina) on a Nextseq 500 (Illumina).
scRNA-Seq: For droplet-based scRNA-seq, 7,000 cells (sorted uNK or total unsorted cells) were loaded onto the Chromium Single Cell 3’ Chip A (10x Genomics) and processed through the chromium controller to generate Gel beads in Emulsion. RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics) as per the manufacturer’s instructions. Libraries were sequenced on an Illumina Hi-Seq.

tag: tissue

value: mouse maternal-fetal interface

tag: genotype

tag: sample id

tag: mouse id

tag: technology

value: full length (SS2) scRNa-Seq

tag: atlas

value: maternal-fetal NK interface atlas (SS2)


title: CMU2-164-14

city: Charlottesville

first: Clint

last: Upchurch

email: cmu3yz@virginia.edu, nl2q@virginia.edu

state: VA

address: 1307 Lane Rd.

department: Pharmacology

country: USA

institute: University of Virginia

library_source: transcriptomic

data_processing:
STAR 2.7.2b
Sequences were aligned to GrCM38/mm10 using STAR 2.7.2b
Results from each lane were merged for each sample and reads for each gene were counted using featureCounts
Read counts were normalized and fold change was calculated using EdgeR.
Assembly: mm10
Supplementary files format and content: comma-delimited text files include raw counts for each sample.

molecule: polyA RNA

growth_protocol: AML12 murine hepatocytes (ATCC CRL-2254) were cultured in DMEM:F12 supplemented with 10% FBS (R&D Systems S12450/Atlanta Biologicals S11150) and 1% Anti-Anti (Gibco 15240-062) and grown at 37°C with 5% CO2. Cells were passaged when they reached 90% confluency using 0.5% Trypsin (Gibco 15400-054).

extract_protocol:
RNA was harvested using RNeasy Kit after tissue lysis using TissueLyzer II in RLT Buffer. RNA samples were quantified using a NanoDrop.
RNA enriched for polyA RNA using Oligo(dT) beads and cDNA libraries were constructed in a strand dependent manner using NEBNext Ultra II RNA Library Prep Kit. cDNA library fragment size was verified using Bioanalyzer 2100 and cDNA libraries were pooled for sequencing.

treatment_protocol: AML12 hepatocytes were treated for four hours with vehicle, truncated OxPAPC, full-length OxPAPC, and OxPAPC (100 ug/mL) solubilized in completed medium as described above.

tag: cell line

tag: cell type

value: Hepatocytes

tag: treatment

value: OxPAPC


title: CMU2-164-13


title: ChAd-27_I-D7

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Trimmed RNA-seq data were aligned to the human V, D and J genes and obtained immune clonotypes using MiXCR (Bolotin et al., Nat Methods, 2015; Bolotin et al., Nat Biotechnol, 2017).
Assembly: hg19
Supplementary files format and content: HTSeq counts from RNA-seq samples

organism: Homo sapiens

source_name: PBMCs

growth_protocol: Blood samples were collected from individuals both prior and after vaccinations.

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated using a Maxwell RSC simply RNA Blood purification kit.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.

tag: age

tag: gender

value: Female

tag: vaccine

value: 1st dose, ChAdOx1

value: PBMCs


title: 15_4G_UtrNK_A153_E9_S153 : SS2 sample


title: 9_5B_UcNK_A96_H12_S96 : SS2 sample

value: filtered out of SS2 NK atlas


title: SCRBd4_1

city: Houston

first: Ellen

last: Busschers

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
mapping using STAR v2.5
quantification using HTSeq V0.6.1
deSeq2
Assembly: mouse mm-10
Supplementary files format and content: xls files contain readcount for each sample
Supplementary files format and content: readcount for each sample in .xls and deSeq2 results for each comparison in .csv

growth_protocol: samples were maintained in ascorbic acid free alpha-MEM with 10% FBS. They were plated at 1.8x10^5 cells per well in a 6 well plate. 24h after plating cells were harvested for d0. then, media containing 50ug/mL ascorbic acis and 10mM b-glyerolphosphate was added for 4 days and cells were harvested on day 4

extract_protocol:
RNA was isolated using Zymo quickRNA miniprep kit following protocol
Library preparation and RNA-seq was performed by by Novogene Co. (Sacramento CA, USA).

treatment_protocol: DMSO and ML-60218 samples were treated for 3 days. From day -1 up to day 2 with either 40uM ML-60218 or an equivalent amount of DMSO. Other samples were infected and selected with noted shRNAs or pInducer20 vectors before plating. For pIndocuer20-empty control and pInducer-MAF1 samples 1uM Doxicycline was added at day -1 and maintained throughout the experiment.

value: stromal cells

value: scramble control for shBrf1

value: osteoblast differentiation


title: 11_3E_UtrNK_A210_B6_S210 : SS2 sample


title: CMU2-164-12

value: Full-length OxPAPC


title: shBRd4_3

value: Brf1 knockdown


title: ChAd-27_I-D0


title: 9_5B_UcNK_A14_B2_S14 : SS2 sample


title: 8_1D_UcNK_A215_B11_S215 : SS2 sample


title: shBRd4_2


title: shBRd4_1


title: ChAd-26_I-D7


title: CMU2-164-10


title: 4_7H_UtrNK_A35_C11_S35 : SS2 sample


title: ChAd-26_I-D2


title: SCRMd4_3

value: scramble control for shMaf1


title: CMU2-164-9


title: SCRMd4_1


title: ChAd-26_I-D0


title: SCRMd4_2


title: CMU2-164-8

value: Truncated OxPAPC


title: 9_3G_UcNK_A380_H8_S380 : SS2 sample


title: ChAd-27_I-D3


title: ChAd-25_I-D7


title: CMU2-164-7


title: shMAd4_3

value: Maf1 knockdown


title: CMU2-164-6


title: 4_7H_UtrNK_A63_F3_S63 : SS2 sample

value: mouse maternal-fetal interface


title: shMAd4_2


title: shMAd4_1


title: ChAd-25_I-D2


title: CMU2-164-11


title: 8_1D_UtrNK_A27_C3_S27 : SS2 sample

value: full length (SS2) scRNa-Seq


title: ChAd-24_I-D7


title: ChAd-25_I-D0


title: CMU2-164-3

value: Vehicle


title: DMSOd0_2

value: DMSO control for ML-60218


title: 11_3E_UtrNK_A264_F12_S264 : SS2 sample


title: ChAd-24_I-D0


title: DMSOd0_3


title: 11_3E_UcNK_A160_F4_S160 : SS2 sample


title: ChAd-24_I-D3


title: 4_7H_UcNK_A243_E3_S243 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: DMSOd0_1


title: ChAd-23_I-D7

value: Female


title: 4_7H_UtrNK_A32_C8_S32 : SS2 sample


title: Mouse 53

data_processing:
STAR 2.7.2b
Sequence reads were trimmed for adapter sequences using TrimGalore
Trimmed sequences were mapped to GrCM38/mm10 using STAR 2.7.2b and reads for each gene were counted using featureCounts
Read counts were normalized and fold change was calculated using EdgeR.
Assembly: mm10
Supplementary files format and content: comma-delimited text files include raw counts for each sample.

source_name: Liver

extract_protocol:
RNA was harvested using RNeasy Kit after tissue lysis using TissueLyzer II in RLT Buffer. RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbard CA, USA) and RNA integrity was checked using Agilent tapeStation 4200 (Agilent Technologies, palo Alto, CA, USA).
RNA enriched for polyA RNA using Oligo(dT) beads and cDNA libraries were constructed in a strand dependent manner using NEBNext Ultra II RNA Library Prep Kit

value: Liver

value: 20 week FPC Diet with interventetion with AAV8-GFP after 6 weeks


title: CMU2-164-4

value: Hepatocytes


title: 15_4G_UcNK_A360_F12_S360 : SS2 sample


title: 9_5B_UtrNK_A269_G5_S269 : SS2 sample


title: ML_d0_3

value: stromal cells

value: 40uM ML-60218 treatment for 3 days (d-1 to d2)


title: ChAd-23_I-D3

value: 1st dose, ChAdOx1

value: PBMCs


title: ChAd-23_I-D0


title: 9_3G_UtrNK_A183_H3_S183 : SS2 sample


title: Mouse 47


title: 8_1D_UtrNK_A80_G8_S80 : SS2 sample


title: Mouse 74

value: 20 week FPC Diet with interventetion with AAV8-scFv-E06 after 6 weeks


title: 9_3G_UcNK_A292_A4_S292 : SS2 sample

value: filtered out of SS2 NK atlas


title: Mouse 75


title: ChAd-22_I-D7


title: CMU2-164-2


title: Mouse 54


title: ChAd-22_I-D3


title: Mouse 51


title: pIndd0_3

value: empty control for MAF1 overexpression

value: osteoblast differentiation


title: Muscle-DQ-4

city: Rochester

first: Xu

last: Zhang

state: MN

address: 200 First St SW

department: Physical Medicine and Rehabilitation

institute: Mayo Clinic

data_processing:
Base-calling was performed using Illumina's RTA version 2.7.7. Raw RNA sequencing paired-end reads were processed through the Mayo RNA-Seq bioinformatics pipeline, MAP-RSeq version 3.1.3. In this process, the fast, accurate and splice-aware aligner, STAR (v2.6.1c), was used to align reads to the reference mouse genome build mm10. Subsequently, gene and exon expression quantification was performed using the Subread featureCounts (v1.5.1) [3] package to obtain both raw and normalized (FPKM - Fragments Per Kilobase per Million mapped) reads.
Genome_build: mm10
Supplementary_files_format_and_content: a table of raw counts of all samples

source_name: Skeletal muscle

extract_protocol:
Quadriceps muscle were collected in Trizol solution (Invitrogen, Carlsbad, CA, USA) and RNA isolation was performed following the instructions.
cDNA libraries were prepared according to the manufacturer’s instructions for the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA). The concentration and size distribution of the completed libraries were determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA).

tag: stain

value: 24 month

tag: agent

value: senolytics


title: 9_3G_UtrNK_A180_G12_S180 : SS2 sample

value: mouse maternal-fetal interface

value: full length (SS2) scRNa-Seq


title: pIndd0_1


title: pIndd0_2


title: Muscle-DQ-3


title: MAF1d0_3

value: MAF1 overexpression


title: ChAd-21_I-D7

value: Female


title: ML_d0_2


title: 11_1i_UcNK_S3 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: ML_d0_1


title: Muscle-DQ-2


title: ChAd-21_I-D3


title: 11_1i_UcNK_A35_C11_S35 : SS2 sample


title: Muscle-DQ-1


title: ChAd-21_I-D0


title: 11_3E_UtrNK_A270_G6_S270 : SS2 sample


title: MAF1d0_2


title: MAF1d0_1


title: ChAd-22_I-D0


title: Muscle-Old-4

value: vehicle


title: ChAd-20_I-D3


title: 11_3E_UcNK_A132_C12_S132 : SS2 sample


title: Muscle-Old-3


title: SCRBd0_1

value: scramble control for shBrf1


title: Muscle-Old-2


title: ChAd-20_I-D0


title: SCRBd0_3

value: stromal cells


title: 11_1i_UcNK_A19_B7_S19 : SS2 sample


title: 11_1i_UcNK_A34_C10_S34 : SS2 sample


title: 15_4G_UtrNK_A180_G12_S180 : SS2 sample


title: shBRd0_3

value: Brf1 knockdown


title: SCRBd0_2


title: ChAd-19_I-D7

value: 1st dose, ChAdOx1


title: Muscle-Old-1


title: Muscle-Young-4

value: 6 month


title: 8_1D_UcNK_A283_H7_S283 : SS2 sample


title: shBRd0_1


title: Muscle-Young-3


title: ChAd-19_I-D0

value: PBMCs


title: ChAd-20_I-D7


title: ChAd-18_II-D2

value: Male

value: 2nd dose, ChAdOx1


title: 9_3G_UcNK_A383_H11_S383 : SS2 sample

value: filtered out of SS2 NK atlas


title: Muscle-Young-2


title: shBRd0_2

value: osteoblast differentiation


title: SCRMd0_3

value: scramble control for shMaf1


title: 11_1i_UcNK_A60_E12_S60 : SS2 sample

value: mouse maternal-fetal interface


title: Muscle-Young-1


title: ChAd-18_II-D0


title: 11_1i_UtrNK_A321_C9_S321 : SS2 sample

value: full length (SS2) scRNa-Seq


title: SCRMd0_2


title: 15_4G_UtrNK_A158_F2_S158 : SS2 sample


title: ME11_V2_02Fix

city: New Haven

first: Yanxiang

last: Deng

state: CT

address: 55 Prospect Street

department: Biomedical Engineering

institute: Yale University

description:
ME11_V2_02Fix_CKDL200165545-1a-N702_HF2KTBBXX_L8
This sample was used only for protocol validation. Images and associated files were not generated for this sample.

library_source: genomic

data_processing:
Two constant linker sequences (linker 1 and linker 2) were used to filter Read 1, and the filtered sequences were transformed to Cell Ranger ATAC format (10x Genomics). The genome sequences were in the new Read 1, barcodes A and barcodes B were included in new Read 2. Resulting fastq files were aligned to the mouse reference (mm10) or human reference (GRCh38), filtered to remove duplicates and counted using Cell Ranger ATAC v1.2. The BED like fragments file were generated for downstream analysis. The fragments file contains fragments information on the genome and tissue location (barcode A x barcode B).
Genome_build: mm10
Supplementary_files_format_and_content: BED like fragments file for downstream analysis. The fragments file contains fragments information on the genome and tissue location (barcode A x barcode B).

molecule: genomic DNA

source_name: Mouse embryo E11

extract_protocol:
The fresh frozen tissue section on a standard aminated glass slide was first fixed with formaldehyde. Tn5 transposition was then performed, and adapters containing a ligation linker were inserted to transposase accessible genomic DNA. Afterwards, a set of DNA barcode A solutions were loaded via an array of microchannels 8 to the tissue section for in situ ligation of a distinct spatial barcode Ai (i = 1-50). Then, a second set of barcodes Bj (j = 1-50) were introduced on the tissue surface in microchannels perpendicularly to those in the first flow barcoding step. These barcodes were then ligated at the intersections, resulting in a mosaic of tissue pixels, each of which contains a distinct combination of barcodes Ai and Bj (i = 1-50, j = 1-50).
During each flow or afterward, the tissue slides were imaged under the microscope such that spatially barcoded accessible chromatin can be correlated with the tissue morphology. After forming a spatially barcoded tissue mosaic (n = 2500), reverse crosslinking was performed to release barcoded DNA fragments and library construction was completed during the PCR. NGS sequencing was then performed using a HiSeq sequencer with pair-end 150 bp mode with custom read 1 primer.

value: E11 Embryo

tag: spatial resolution

value: 50 um


title: ChAd-19_I-D3

value: Female


title: 8_1D_UcNK_A255_F3_S255 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: SCRMd0_1


title: ChAd-18_I-D3


title: ME11_V2

description:
ME11_V2_CKDL200159463-1A-N703_HC7VYBBXX_L8
This sample was used only for protocol validation. Images and associated files were not generated for this sample.


title: ChAd-18_I-D7


title: shMAd0_3

value: Maf1 knockdown


title: ChAd-17_I-D7


title: shMAd0_2

value: stromal cells


title: Old Muscle-scRNAseq-rep3

data_processing:
For scRNA-seq, raw data were processed with Cell Ranger (v3.0) (10X Genomics) and aligned to the mouse genome version mm10. Further analyses were carried out in R version 3.6.0 using the package Seurat version (v3.1.3)
Genome_build: mm10
Supplementary_files_format_and_content: tar file include barcodes.tsv, features.tsv, and matrix.mtx files from CellRanger

extract_protocol:
Single cell suspensions for scRNA-seq were prepared from skeletal muscle using Skeletal Muscle Dissociation Kit (Miltenyi, cat 130-098-305). Briefly, quadriceps, gastrocnemius, and tibialis anterior muscle were dissected and cut into small pieces in DMEM containing enzyme D, P, and A. Tissue were digested in gentleMACS C Tube for 1 hour using the program 37C_mr_SMDK_1. After digestion, cells were filtered through 70 μm and then 40 μm strainer. Cells were treated with Red Blood Cell Lysis Solution (Miltenyi, cat 130-094-183) for 2 mins and collected for further processing.
For scRNA-seq, the GEMs were collected for reverse transcription using Chromium Single Cell 3’ Reagent Kits (10X Genomics). Standard Illumina sequencing primers and a unique i7 Sample index were added to each cDNA for library construction.

tag: strain

value: 24 month

value: Mononuclear cells mix


title: ChAd-18_I-D0

value: 1st dose, ChAdOx1


title: shMAd0_1


title: ME11_V1

description:
ME11_V1_S3_L002
This sample was used only for protocol validation. Images and associated files were not generated for this sample.


title: 9_3G_UtrNK_A182_H2_S182 : SS2 sample


title: 4_7H_UcNK_A217_C1_S217 : SS2 sample


title: Old Muscle-scRNAseq-rep2


title: ChAd-17_I-D3

value: PBMCs


title: Neuron_HDM_rep2_TRG

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

country: Japan

institute: Chiba univercity

description: 10x Genomics

data_processing:
Cell Ranger
Assembly: mm10, hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Trigeminal nerve

extract_protocol:
White blood cells of CD45+CD31- fractions that were freshly prepared from mice conjunctival tissue and sorted using a BD FACS Aria III (10,000 cells each, cell viability >98%). Neuron Cells of CD45-CD31- and live cell+ fractions that were freshly prepared from trigeminal nerve tissue of mice and sorted using a BD FACS Aria III (10,000 cells each, cell viability >98%). White blood cells of CD45+ and CD4+ fractions that were freshly prepared from Giant papillae from patients
Libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3 according to manufacturer’s protocol (10X Genomics). The generated scRNA-seq libraries were sequenced using a 128 cycle (paired-end reads) with a NovaSeq 6000 (Illumina).

value: Trigeminal nerve

value: Neuron

value: HDM


title: ChAd-17_I-D0


title: Old Muscle-scRNAseq-rep1


title: 9_5B_UcNK_A11_A11_S11 : SS2 sample


title: Neuron_HDM_rep1_TRG

description: 10x Genomics


title: 11_3E_UcNK_A175_G7_S175 : SS2 sample

value: filtered out of SS2 NK atlas


title: 9_3G_UcNK_A339_E3_S339 : SS2 sample


title: ChAd-16_I-D7


title: 15_4G_UcNK_A325_D1_S325 : SS2 sample


title: Young Muscle-scRNAseq-rep3

value: 6 month


title: 4_7H_UcNK_A263_F11_S263 : SS2 sample

value: mouse maternal-fetal interface


title: ChAd-16_I-D4


title: 9_3G_UcNK_A317_C5_S317 : SS2 sample

value: full length (SS2) scRNa-Seq


title: CD45+_conjunctival_tissue_Saline_mice

description: 10x Genomics

source_name: conjunctival tissue

value: conjunctival tissue

value: Saline


title: ChAd-16_I-D0

value: Female


title: CD45+_conjunctival_tissue_HDM_mice

description: 10x Genomics


title: U_TDP

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
Metrics for TCRs were generated via VDJTools v1.2.1
Assembly: mm10
Library strategy: Bulk TCR sequencing

source_name: Tumor infiltrating T cells

growth_protocol: B16F10 melanoma cells (2x105 cells) were implanted subcutaneously in 0.2ml of matrigel in C57/BL/6 mice.  Tumors were resected 11 days later and  CD4+, CD8+ and CD4+CD8+ TILS were FACs sorted.

extract_protocol:
RNA was extracted from purified open repertoire mouse CD4+, CD8+, and CD4+CD8+ TILs FACS sorted from B16 tumors. Purified RNA samples were quantified using Qubit RNA HS Assay Kit (Thermo Fisher Scientific Cat. No. Q32852). The Agilent 2100 Bioanalyzer and Agilent RNA 600 Nano Kit were used to quantify and evaluate RNA integrity.
25ng of total RNA was reverse transcribed using the Ion Torrent™ NGS Reverse Transcription Kit (Thermo Fisher Scientific Cat. No. A45003). For each sample, 25ng cDNA was amplified using Ion AmpliSeq™ Mouse TCR Beta SR Assay (RNA) (Thermo Fisher Scientific Cat. No. A45489), and protocol as described in the Ion AmpliSeq™ Mouse Immune Repertoire User Guide (MAN0018524 rev. B.0). Libraries were purified with Agencourt AMPure XP beads (Beckman Coulter Cat. No. A63880), washed with 70% ethanol, and eluted in 50uL Low TE buffer. Resulting library samples were diluted 1:100 and quantified using the Ion Library Quantification Kit (Thermo Fisher Scientific Cat. No. 4468802), then diluted to 25pM with Low TE buffer. Samples were pooled and sequenced using the Ion 540 chip to a target depth between 2-3M reads, followed by analysis via Ion Reporter version 5.12. TCR sequencing the Illumina-based platform was performed by Sequenta as described in Klinger et al.33, the ImmunoSeq assay (Adaptive Biotechnologies) or Archer Immunoverse HS TCRB assay, per manufacturer instruction.

value: Tumor infiltrating T cells

value: Untreated


title: ChAd-15_I-D4


title: ChAd-15_I-D7


title: U_CD8


title: Myofiber-Old-p21-High-rep3

data_processing:
Base-calling was performed using Illumina’s RTA version 2.7.7. Sequences in FASTQ files were mapped to the mouse genome (mm10) using Tophat2 (v.2.1.1). Gene raw counts and normalized counts (FPKM) were generated using RseQC (v.2.3.6).
Genome_build: mm10
Supplementary_files_format_and_content: a table of raw counts of all samples

extract_protocol:
Single myofibers for bulk-RNA-seq were isolated as previously described (Gallot, Y.S., et al., Isolation, Culture, and Staining of Single Myofibers. Bio Protoc, 2016. 6(19).), with a little modification. Briefly, extensor digitorum longus (EDL) muscle was collected and digested in DMEM with 2.5% HEPES, 1% Penicillin (Pen)/streptomycin (Strep) solution, and 400 U/ml of collagenase II for 2 hours in an incubator at 37 °C and 5% of CO2. Single myofibers were flushed and transferred with sterile Pasture pipette into DMEM with 10% FBS, 1% Pen/Strep, 2% CEE, and 10 ng/ml bFGF. After washed for four times in medium, single myofibers were transferred to Trizol solution (Invitrogen, Carlsbad, CA, USA) for RNA isolation.
Full length double-stranded cDNA was prepared from 1ng of total RNA according to the manufacturer’s instructions for the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). Indexed cDNA libraries using 150pg input cDNA were prepared using the Nextera XT DNA Library Preparation Kit (Illumina product number FC-131-1096). The cDNA was fragmented, and Illumina sequencing adapters were added in a single tagmentation step using Nextera XT transposome. Tagmented cDNA was amplified and final indexes were added using 12 cycles of PCR followed with a 3:2 Ampure bead purification.

value: Myofiber

tag: molecule p21 expression level

value: High


title: U_CD4


title: Myofiber-Old-p21-High-rep4

value: 24 month


title: mouse EPN cells, ChIP-Sox9

first: Debosmita

last: Sardar

data_processing:
Quality control was performed using fastQC (v0.11.17) and MultiQC (v0.9).
Reads were mapped to the mouse genome mm10 or human genome hg38 assembly using bowtie2
Using the HOMER software suite, bedgraph files and tag directories were made
findPeaks command in histone (for H3K27ac) or factor (for Sox9) mode was used to filter ChIP peaks enriched over Input control
Annotation of enriched peaks was performed using annotatePeaks with mm10 or hg38 assembly
Assembly: Integrated Genome Browser compatible files were made using samtools, sort and index, deepTools bamCompare
Supplementary files format and content: mm10; hg38
Supplementary files format and content: bw, narrowPeak

source_name: derived from Rela fusion EPN

extract_protocol:
Tissue was dissociated, crosslinked with 1.1% formaldehyde for 10 min, quenched and frozen. After thawing, cells were lysed to release nuclei, followed by nuclear lysis. Lysates were sonicated using a Diagenode Bioruptor.
ChIP-Seq libraries were prepared using the TruSeq ChIP Library Preparation Kit (Ilumina, IP-202-1012). 10 ng of DNA was used as starting material for Input and IP samples. Libraries ranging from 250-350 bp were extracted from agarose gel incisions and PCR amplified for 18 cycles. Libraries were purified using AMPure XP beads and library quality was validated using a Standard Sensitivity NGS Fragment Analysis Kit.

tag: tissue

value: derived from Rela fusion EPN

value: control

value: EPN control


title: Myofiber-Old-p21-High-rep2


title: ChAd-15_I-D0

value: 1st dose, ChAdOx1

value: PBMCs


title: DPTCells_HTO_CD4+,CD8+,CD4+CD8+,CD8+CD4+

description: 10x HTO

data_processing:
Filtered gene expression matrices were generated using 10X CellRanger (version 3.1.0).
Paired single-cell VDJ sequences and annotations were generated using 10X Cellranger VDJ (version 3.1.0) and high confidence sequences were mapped to gene expression barcodes.
Feature barcode matrices were generated for each sample (consisting of five mice) using antibody barcode patterns from TotalSeq.
Mouse specific barcodes were demultiplexed by HTO using Seurat (version 3.2.3).
Assembly: mm10 (GENCODE vM23/Ensembl 98)

source_name: Sorted T cells from B16 melanoma resections

growth_protocol: B16F10 melanoma cells (2x105 cells) were implanted subcutaneously in 0.2ml of matrigel. Tumors were resected 11 days later and CD45.1 CD4+ and CD4+CD8+, and CD45.2 CD8+ and CD8+CD4+ TILS were FACs sorted.

extract_protocol:
Intra-tumor CD45.1+ CD4+, CD45.1+ CD4+CD8+, CD45.2+ CD8+, and CD45.2+ CD8+CD4+ T cells were sorted as individual populations from the tumors of 10 pooled mice. Sorted T cells were individually hashtagged and counted. Approximately equal numbers of each cell population were pooled togther as one sample for sequencing.   Sorted T cells were stained with Trypan blue and the Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following QC, the single cell suspension was loaded onto Chromium Next GEM Chip K (10X Genomics PN 1000286) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 6,200 cells proceeded using the Chromium Next GEM Single Cell 5’ Kit v2 (10X Genomics PN 1000263) according to the manufacturer’s protocol. cDNA amplification included 14 cycles and 10.6ng of the material was used to prepare a sequencing library with 16 cycles of PCR. The indexed library was pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/91 run using the NovaSeq 6000 SP Reagent Kit (100 cycles) (Illumina). 194 million paired reads were generated for the sample.
An aliquot of cDNA generated using the methods described above was used to enrich for V(D)J regions using the Chromium Single Cell Mouse TCR Amplification Kit (10X Genomics PN 1000254) according to the manufacturer’s protocol with 10 cycles of PCR during enrichment and 9 cycles during library preparation. The indexed library was pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/91 run using the NovaSeq 6000 SP Reagent Kit (100 cycles) (Illumina). 39 million paired reads were generated for the sample. Amplification products generated using the methods described above included both cDNA and feature barcodes tagged with cell barcodes and unique molecular identifiers. Smaller feature barcode fragments were separated from longer amplified cDNA using a 0.6X cleanup using aMPure XP beads (Beckman Coulter catalog # A63882). Libraries were constructed using the 5’ Feature Barcode Kit (10X Genomics PN 1000256) according to the manufacturer’s protocol with 9 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/91 run using the NovaSeq 6000 SP Reagent Kit (100 cycles) (Illumina). 72 million paired reads were generated for the sample.
scRNA/TCR sequencing with hasthtag and feature barcoding

treatment_protocol: 1 day following tumor implantation, 1x10^6 purified CD45.1 CD4+ or CD45.2 CD8+ T cells were intravenously injected into the tail vein in 100ul PBS.

tag: congenic marker

value: untreated

tag: dna id

tag: dna barcode


title: Young Muscle-scRNAseq-rep2

value: 6 month

value: Mononuclear cells mix


title: ChAd-14_I-D7


title: Young Muscle-scRNAseq-rep1


title: Myofiber-Old-p21-High-rep1


title: DPTCells_VDJ_CD4+,CD8+,CD4+CD8+,CD8+CD4+

description: 10x VDJ


title: Myofiber-Old-p21-Low-rep3

value: Low


title: ChAd-14_I-D4


title: 9B

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2018_1 were also provide

source_name: Preimplantation embryo

growth_protocol: The embryos were thawed using Quinn’s Advantage thaw kit according to the manufacturer’s instructions (Sage). After thawing, the embryos were cultured in 40-ml microdrops of Quinn’s medium supplemented with 10% synthetic protein serum substitute (Sage) under mineral oil (Sage) at 37˚C in 5% CO2 and 5% O2 in a humidified atmosphere.

extract_protocol:
cDNA has been prepared using SMARTer® Ultra® Low Input RNA for Illumina® Sequencing – HV (Clontech) directly from cells. All experiments were carried out in a PCR clean workstation using protocols provided by the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treated embryos were exposed from thawing till harvesting to 10-7 M T3 (Sigma). The medium was refreshed on a daily basis.

value: trophectoderm (TE)


title: DPTCells_RNA_CD4+,CD8+,CD4+CD8+,CD8+CD4+

description: 10x scRNA


title: 8B


title: Myofiber-Old-p21-Low-rep2


title: Lymph_node_endogenous_VDJ

description: 10x VDJ

data_processing:
Filtered gene expression matrices were generated using 10X CellRanger (version 3.1.0).
Paired single-cell VDJ sequences and annotations were generated using 10X Cellranger VDJ (version 3.1.0) and high confidence sequences were mapped to gene expression barcodes.
Assembly: mm10 (GENCODE vM23/Ensembl 98)

source_name: Sorted CD4+ and CD4+CD8+ T cells from B16 melanoma resections

growth_protocol: B16F10 melanoma cells (2x105 cells) were implanted subcutaneously in 0.2ml of matrigel.  Tumors were resected 11 days follow adoptive cell transfer and TRP1 (CD45.1) CD4+ and CD4+CD8+ TILS were FACs sorted.

extract_protocol:
Sorted T cells were stained with Trypan blue and the Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following QC, the single cell suspension was loaded onto Chromium Next GEM Chip K (10X Genomics PN 1000286) and GEM generation, cDNA synthesis, abd cDNA amplification.
Library preparation of 8,100 cells proceeded using the Chromium Next GEM Single Cell 5’ Kit v2 (10X Genomics PN 1000263) according to the manufacturer’s protocol. cDNA amplification included 13 cycles and 32ng of the material was used to prepare a sequencing library with 14 cycles of PCR. The indexed library was pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/91 run using the NovaSeq 6000 SP Reagent Kit (100 cycles) (Illumina). 228 million paired reads were generated for the sample.

treatment_protocol: Cyclophosphamide (CTX) monohydrate mixed in sterile PBS was administered intraperitoneally as a single dose at 250mg/kg once tumors were established (1-2 weeks later). 1 day following CTX injection, 1x10^6 purified TRP1 CD4+ T cells were intravenously injected into the tail vein in 100ul PBS.

value: RAG1- BW TRP-1 TCR


title: 7B


title: ChAd-12_I-D7

value: Male


title: ChAd-14_I-D0

value: Female


title: Myofiber-Old-p21-Low-rep1


title: Tumor_transgenic_endogenous_VDJ

description: 10x VDJ

value: Tumor infiltrating T cells


title: 4B


title: 6B


title: ChAd-12_I-D4


title: ChAd-12_I-D0


title: Lymph_node_endogenous_RNA

description: 10x scRNA


title: 11B


title: Myofiber-Young-p21-Low-rep3

value: Myofiber


title: Myofiber-Young-p21-Low-rep2


title: 10B


title: CRC_4 °C 2

city: STOCKHOLM

first: Kayoko

last: Hosaka

state: Solna

address: Solnavägen 9

department: MTC

country: Sweden

institute: Karolinska institutet

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCm38
Supplementary files format and content: csv file includes read counts for each sample.

source_name: Tumor tissue

extract_protocol:
Total RNA was extracted from fresh tissue samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100.
200 ng RNA for each group was used for the library construction by a TruseqTM RNA sample prep Kit (Illumina, San Diego, CA, USA). The constructed DNA was enriched by PCR amplification and then purified by Certified Low Range Ultra Agarose (Bio-Rad, Hercules, CA, USA) gel electrophoresis. Clone clusters were generated on Illumina cBot, using Truseq PE Cluster Kit v3-cBot-HS.

value: Tumor tissue

value: Exposed to 4C 2 weeks


title: ChAd-11_I-D7


title: 2B


title: Myofiber-Young-p21-Low-rep1


title: Tumor_transgenic_endogenous_RNA

description: 10x scRNA


title: CRC_4 °C 1


title: ChAd-11_I-D4


title: ME13_50um

data_processing:
Two constant linker sequences (linker 1 and linker 2) were used to filter Read 1, and the filtered sequences were transformed to Cell Ranger ATAC format (10x Genomics). The genome sequences were in the new Read 1, barcodes A and barcodes B were included in new Read 2. Resulting fastq files were aligned to the mouse reference (mm10) or human reference (GRCh38), filtered to remove duplicates and counted using Cell Ranger ATAC v1.2. The BED like fragments file were generated for downstream analysis. The fragments file contains fragments information on the genome and tissue location (barcode A x barcode B).
Genome_build: mm10 (GRCm38), GRCh38
Supplementary_files_format_and_content: BED like fragments file for downstream analysis. The fragments file contains fragments information on the genome and tissue location (barcode A x barcode B).

source_name: Mouse embryo E13

extract_protocol: The fresh frozen tissue section on a standard aminated glass slide was first fixed with formaldehyde. Tn5 transposition was then performed, and adapters containing a ligation linker were inserted to transposase accessible genomic DNA. Afterwards, a set of DNA barcode A solutions were loaded via an array of microchannels 8 to the tissue section for in situ ligation of a distinct spatial barcode Ai (i = 1-50). Then, a second set of barcodes Bj (j = 1-50) were introduced on the tissue surface in microchannels perpendicularly to those in the first flow barcoding step. These barcodes were then ligated at the intersections, resulting in a mosaic of tissue pixels, each of which contains a distinct combination of barcodes Ai and Bj (i = 1-50, j = 1-50). During each flow or afterward, the tissue slides were imaged under the microscope such that spatially barcoded accessible chromatin can be correlated with the tissue morphology. After forming a spatially barcoded tissue mosaic (n = 2500), reverse crosslinking was performed to release barcoded DNA fragments and library construction was completed during the PCR. NGS sequencing was then performed using a HiSeq sequencer with pair-end 150 bp mode with custom read 1 primer.

value: E13 embryo

value: 50 um


title: CRC_30 °C 3

value: Exposed to 30C 2 weeks


title: 9A

value: inner cell mass (ICM)


title: 1B

value: control


title: ChAd-11_I-D0

value: 1st dose, ChAdOx1

value: PBMCs


title: ME11_50um

value: E11 embryo


title: CRC_30 °C 2


title: ChAd-10_I-D7


title: 7A


title: 6A


title: ChAd-10_I-D4


title: CRC_30 °C 1


title: ChAd-10_I-D0


title: 5A


title: ChAd-9_I-D7


title: 4A


title: ME13_50um_2


title: P21_brain

data_processing:
Two constant linker sequences (linker 1 and linker 2) were used to filter Read 1, and the filtered sequences were transformed to Cell Ranger ATAC format (10x Genomics). The genome sequences were in the new Read 1, barcodes A and barcodes B were included in new Read 2. Resulting fastq files were aligned to the mouse reference (mm10) or human reference (GRCh38), filtered to remove duplicates and counted using Cell Ranger ATAC v1.2. The BED like fragments file were generated for downstream analysis. The fragments file contains fragments information on the genome and tissue location (barcode A x barcode B).
Assembly: mm10 (GRCm38), GRCh38
Supplementary files format and content: BED like fragments file for downstream analysis. The fragments file contains fragments information on the genome and tissue location (barcode A x barcode B).

source_name: Mouse brain P21

value: Mouse brain

value: 20 um


title: sg5-rep2

city: Singapore

first: Pushkar

last: Dakle

address: 14 Medical Drive, #12-01,

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
100 bp paired-end reads were aligned to murine reference transcriptome (GRCm38/mm10; Ensemble version 84) using Kallisto (version 0.43.0).
Differential analysis was performed using DESeq2. Gene expression was quantified in FPKM units using DESeq2 FPKM command and was used for all downstream analysis and plotting.
Genome_build: mm10
Supplementary_files_format_and_content: Expression abundances in terms of FPKM as measured by DESeq2

source_name: 32D cells transduced with dCas9-KRAB-sg2 (replicate 2)

growth_protocol: 32D cells were cultured in IMDM medium with 1ng/mL IL3

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit.
Libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer’s protocol and sequenced on HiSeq 4000 (Illumina).

treatment_protocol: Cells were transduced with Lentiviral particles (EV or sg2/sg5) and selcted with puromycin for a week.

value: murine myeloid cells

tag: genotype/variation


title: ME11_20um

value: Embryo


title: 2A


title: sg5-rep1

source_name: 32D cells transduced with dCas9-KRAB-sg5 (replicate 1)


title: sg2-rep2


title: sg2-rep1

source_name: 32D cells transduced with dCas9-KRAB-sg2 (replicate 1)


title: ChAd-9_I-D4

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Trimmed RNA-seq data were aligned to the human V, D and J genes and obtained immune clonotypes using MiXCR (Bolotin et al., Nat Methods, 2015; Bolotin et al., Nat Biotechnol, 2017).
Assembly: hg19
Supplementary files format and content: HTSeq counts from RNA-seq samples

source_name: PBMCs

value: Female


title: Sample_2 surface protein

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: Pool of cells from 5 wild-type animals (labeled with BioLegend HTO antibody TotalSeq-B0301 to B0305) and cells from 5 IL20RB knock-out animals (labeled with antibodies B0306-B0310)

data_processing:
Library and cell barcode demultiplexing, read alignment to the mouse transcriptome (Ensembl release 98) and generation of the table of UMI counts were performed using Cellranger (version 6.0.1).
Further processing of the UMI counts table was performed by using R 4.0.5 and Bioconductor 3.12 packages, notably DropletUtils (version 1.10.3), scran (version 1.18.7) and scater (version 1.18.6), following mostly the steps illustrated in the Bioconductor OSCA book (https://bioconductor.org/books/release/OSCA/)
Cell were demultiplexed into their samples of origin using the function hashedDrops from the DropletUtils package (with default parameters except min.prop=0.01, and providing as input the relative abundances of HTOs in the ambient solution). Based on the observed distributions, cells with 0% or more than 10% of UMI  counts attributed to the mitochondrial genes 25, with less than 1,000 UMI counts, or with less than 500 detected genes were excluded. Doublets identified with the hashedDrops function or with the scDblFinder package (version 1.4.0) were excluded. A total of 2,633 IL20RB KO cells and 3,421 WT cells were retained.
Genome_build: mm10
Supplementary_files_format_and_content: UMIsMatrix.txt.gz: compressed tab-separated file with UMI counts for Ensembl release 98 gene models and demultiplexed cells; column headers include the cell barcode sequence and the library (well) ID separated by a dash, followed by the condition and sample ID separated by underscores (e.g., "AAACCCAAGGTCGAGT-1_KO_B0310").
Supplementary_files_format_and_content: features.csv: comma-separated file with barcode information on hashtagging antibodies used for different samples.

source_name: Esophagus CD45+ immune cells

growth_protocol: Animals were bred and mainained under specific pathogen-free (SPF) conditions in the animal facility of the Department of Biomedicine at the University of Basel in Switzerland.

extract_protocol:
Extracted mouse esophageal samples were washed in PBS, minced in small pieces, and digested in Roswell Park Memorial Institute (RPMI) 1640 (Sigma-Aldrich) containing 0.5mg/ml collagenase IV and 10U/ml DNase I for 30mins in a shaking (200rpm) water bath at 37°. Digested tissue was filtered through a 70uM cell strainer (Sarstedt). The single-cell suspension was centrifuged 5mins at 600xg (4°C) and transferred to conical 96-well plates (Sarstedt) for further analysis by flow cytometry.
Esophagus cell suspensions from five wild-type animals were labeled with BioLegend hashtaging antibodies TotalSeq-B0301 to B0305, while suspensions from five IL20RB[-/-] animals were labeled with antibodies TotalSeq-B0306-B0310. The cells suspensions were pooled and the resulting suspesnion was sorted for viable CD45+ cells using flow cytometry.
Cells were loaded on 2 wells of a 10× Genomics Chromium Single Cell Controller with volumes aiming at a targeted recovery of 10,000 cells per well, and 3’end libraries were generated using v3 chemistry
Sequencing was performed on 2 lanes of an SP flow-cell of an Illumina NovaSeq 6000 sequencer at the Genomics Facility Basel of the ETH Zurich (with 90nt-long R2 reads), with a mix of 90% cDNA libraries and 10% HTO libraries

treatment_protocol: To induce an EoE mouse model, mice were sensitized by treating the ear with 1 nmol MC903 (calcipotriol; Tocris) in absolute ethanol and 5 mg/mL OVA Grade 5 (Sigma) in PBS, repeated daily for 14 days. At day 14 the drinking water was replaced with autoclaved water containing 1.5 g OVA / l and given for four days. At days 15 and 17, the mice were additionally challenged by gavage with 50 mg OVA in 100 µl water. Mice were sacrificed for organ collection at day 18.

value: CD45+ immune cells


title: Sample_1 surface protein


title: ChAd-9_I-D0

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated using a Maxwell RSC simply RNA Blood purification kit.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.


title: EV-rep2

source_name: 32D cells transduced with dCas9-KRAB-EV (replicate 2)


title: ChAd-8_I-D7


title: Gard_rep5

city: St. Louis

first: Nicole

last: Gilbert

state: MO

address: 425 S Euclid Ave

institute: Washington University School of Medicine

data_processing:
Illumina HiSeq 2500 reads demultiplexed using a custom demultiplexing script written in Python and then aligned to the Ensembl GRCm38.76 (Mus musculus) assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5
Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction, known junction saturation and read distribution over known gene models with RSeQC version 2.3.
All gene-level and transcript counts were then imported into the R/Bioconductor package EdgeR and TMM-normalized to adjust for differences in library size.
Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: bladder

extract_protocol:
Bladders were removed, flash frozen in liquid nitrogen, RNA was extracted using RNeasy Plus Mini kit (Qiagen). ds-cDNA was prepared from 10ng total RNA using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: wild type

tag: bladder exposure

value: G. vaginalis


title: EV-rep1

source_name: 32D cells transduced with dCas9-KRAB-EV (replicate 1)

tag: cell type


title: Sample_2 biological


title: Gard_rep4


title: ChAd-8_I-D4


title: ImR tumor rep3

city: New Orleans

first: Xian-Feng

last: Wang

state: LA

address: 1700 Tulane Avenue

institute: Tulane University

data_processing:
Raw reads were aligned to the Drosophila melanogaster reference genome (dos Santos et al., 2015).
FeatureCounts and DESeq2 were then used to assign gene identity to genomic features, and to analyze fold change (log2(FC)) from count data (Liao et al., 2014; Love et al., 2014).

organism: Drosophila melanogaster

source_name: Salivary gland imagnal ring

growth_protocol: Drosophila lines were maintained and crossed on the BDSC cornmeal food (https://bdsc.indiana.edu/information/recipes/bloomfood.html)

extract_protocol:
Total RNAs were extracted by using Zymo RNA preparation kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Gal80ts was used to control the time for gene expression

value: Salivary gland imagnal ring

tag: developmental stage

value: 7 days at 18 degree+7 days at 29 degree

value: Actts>GFP+NICD


title: ChAd-8_I-D0

tag: age


title: Gard_rep3


title: ImR tumor rep2


title: Aged_4

city: Providence

first: Kaitlyn

last: Hajdarovic

state: RI

address: 69 Brown St

department: Neuroscience

institute: Brown University

data_processing:
We performed sequence alignment to the mm10 genome (2020) using the CellRanger (cellranger/6.0.0) software from 10x Genomics with the –include introns flag. The resulting feature-barcode matrices were read into R version 4.1.0, excluding any nuclei expressing fewer than 200 genes, and any gene expressed in fewer than three nuclei. Filtering and visualization were performed using Seurat (4.0.3). For samples sequenced on an Illumina HiSeq, nuclei with fewer than 200 or more than 3000 features were filtered out. For samples sequenced on the NovaSeq, nuclei with fewer than 200 or more than 7500 features were filtered out. Similarly, nuclei with greater than 10% mitochondrial mapping were removed, resulting in 23,808 nuclei in the aged condition, and 16,256 nuclei in the young condition. Integration of the datasets was performed using the IntegrateData function on 5000 variable features.
Genome_build: mm10 genome (2020)
Supplementary_files_format_and_content: processed data shared as an R data object (.RDS). The data object is a seurat object containing two assays (RNA and integrated) with all metadata for each sample.

molecule: nuclear RNA

source_name: National Institute on Aging

extract_protocol:
Prepared with 10x genomics V3 kit, sequenced on Ilumina Novaseq, dual index
Two whole hypothalamuses were pooled into each biological replicate, for a total of tfour replicates for the young and aged conditions. Nuclei extraction was performing using the Nuclei Isolation Kit: Nuclei PURE Prep Kit (Millipore Sigma) according to the manufacturer’s instructions with the following modifications: for each sample, two hypothalamuses were dissected out of the animals and rinsed in cold PBS. Tissue was transferred using a transfer pipette into a refrigerated Dounce homogenizer with 5 mL of lysis solution following kit instructions. Tissue was homogenized with the Dounce B and the lysate was transferred into a 15 mL falcon tube through a 40-micron filter. The sucrose purification step was performed with the following modifications: half the volume of all reagents was used to account for the small tissue samples, an SW34 rotor was used, and samples were spun for 45 minutes at 30,000 X g (13,000 rpm) at 4 °C. Nuclei were counted using a hemocytometer, and 5000 cells per sample were loaded onto the Chromium Single Cell 3′ Chip (10x Genomics) and processed with the Chromium Controller (10x Genomics).
Samples Young _1, Young_2, Aged_1 and Aged_2 were prepared using the Chromium Single Cell 3′ Library & Gel Bead kit v2 according to manufacturer’s instructions. Samples were sequenced at GENEWIZ, Inc on an Illumina HiSeq, with a target of 50,000 reads per sample. The Aged_1 and Young_2 samples underwent an additional round of sequencing to obtain sufficient read depth. Samples Young_3, Young_4, Aged_3, and Aged_4 were prepared with the Next GEM Single Cell 3ʹ Reagent kit (10x Genomics) and sequenced at Genewiz on an Illumina NovaSeq.

value: Aged (19-24 months)

value: hypothalamus

tag: Sex


title: Gard_rep2


title: ChAd-7_I-D4

tag: gender

tag: vaccine


title: ImR tumor rep1


title: ChAd-7_I-D7


title: Aged_3


title: Control rep3

value: third instar larva

value: Actts>GFP


title: 1A

value: inner cell mass (ICM)

tag: treatment

value: control


title: Young_3

value: Young (3 months)


title: Young_4


title: Control rep2


title: Gard_rep1


title: ChAd-7_I-D0

value: 1st dose, ChAdOx1

value: PBMCs


title: PBS_rep4

value: PBS


title: E15.10_CD4_1HSC

city: Boston

first: Clara

middle: F

last: Alves-Pereira

state: MA

address: 450 Brookline Avenue, SM958b

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: monoclonal sample derived from single HSC

data_processing:
Library strategy: WES
Reference preparation: imputed parental genomes were prepared (“pseudogenomes” (Crowley et al., 2015; Zou et al., 2014)) for each organism, using a custom script (all custom software tools mentioned are available on https://github.com/gimelbrantlab/ASEReadCounter_star); VCF file with one allele considered as a reference (maternal C57BL/6 or first phased allele) and the other as an alternative allele. Only heterozygous sites were used.
Alignment: RNA-seq reads were trimmed from nextera adapters with cutadapt v.1.14 using the wrapper trim_galore; reads were then aligned with STAR aligner v.2.5.4a (Dobin et al., 2013) on each of two pseudogenomes, with default threshold on quality of alignment. Only uniquely alligned reads were used.
Allele assigment. Given vcf file with heterozygous positions, coverage over each SNP was calculated using custom script based on samtools mpileup and parsed to obtain the table with allelic counts. Data processing steps from read alignment to allelic counts were based on a modification of the GATK pipeline (Castel et al., 2015), and described in: https://github.com/gimelbrantlab/ASEReadCounter_star
Allele counting per gene. All exons belonging to the same gene were merged into a single gene model based on GTF file (RefSeq GTF file, GRCm38.68, was downloaded from Ensemble ftp://ftp.ensembl.org/pub/release-68/gtf/ (Zerbino et al., 2018)), excluding overlapping regions that belong to multiple genes. This step was based on the GATK pipeline (Castel et al., 2015).
AI point estimate per gene obtained as a proportion of maternal gene counts to total allelic gene counts
Genome_build: mm10
Supplementary_files_format_and_content: allelic counts and allelic imbalance

source_name: mouse thymus T-cells

extract_protocol:
DNA was isolated from sorted cells using Trizol reagent according to the manufacturer`s protocol.
Sequencing libraries were generated using Agilent SureSelect Mouse All ExonV6 kit (Agilent Technologies, CA, USA) following manufacturer’s recommendations and x index codes were added to attribute sequences to each sample.

value: C57BL/6 x CAST/EiJ F1

tag: cells

tag: rna extraction

value: Trizol

tag: number of cells sorted for dna isolation

tag: library replicate

value: female

tag: donor animal

value: donor animal #15

tag: recipient animal

value: recipient animal #15.10


title: Control rep1

tag: tissue

value: Salivary gland imagnal ring


title: PBS_rep3

tag: strain

value: wild type


title: ChAd-6_I-D7

value: Female


title: PBS_rep2

tag: genotype


title: Sample_1 biological

value: CD45+ immune cells


title: ChAd-6_I-D0


title: PBS_rep1

tag: bladder exposure


title: E6.2_B220IgM_50HSCs

description: polyclonal sample derived from 50 HSCs

source_name: mouse spleen B-cells

value: donor animal #6

value: recipient animal #6.2


title: Down syndrome_2

city: Sutia

first: Hidehiro

last: Suginobe

address: 2-2, Yamadaoka

department: Pediatrics

institute: Osaka University

data_processing:
An Illumina HiSeq 2500 platform in 75-base single-end mode was used for sequencing.
Illumina CASAVA 1.8.2 software was used for base calling.
Sequenced reads were mapped to the human reference genome sequence (hg19) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
Fragments per kilobase of exon per million mapped fragments were calculated using Cuffnorm version 2.2.1.
Ingenuity Pathway Analysis was used to identify canonical pathways of differentially expressed genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: iPS derived EC

growth_protocol: iPSC-derived ECs were maintained in MiraCell EC Culture Medium (Takara bio) with antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using NucleoSpin (Takara Bio) following the manufacturer’s procedure.
Library preparation was performed using the TruSeq stranded mRNA sample prep kit (Illumina).

treatment_protocol: Each iPSC line was differentiated to ECs by using MiraCell iPS Cell to Endothelial Cell Differentiation Kit (Takara bio) following the manufacturer's protocol.

value: iPS derived EC

tag: cell type

value: endothelial cells

value: 21 trisomy


title: E6.43_CD4_1HSC

value: recipient animal #6.43


title: Down syndrome_1


title: NK_16.2h_KIRC5F_WTM : cellranger counts

city: Oxford

first: Gurman

last: Kaur

address: Headley Way

institute: University of Oxford

description: RNA-Seq (10X) Cellranger counts, stored as HDF5 file.

data_processing:
RNA-Seq: bcl2fastq v.2.17.1.14, RSEM v.1.2.8
scRNA-Seq: CellRanger v2.1.0 (mkref and mkfastq), CellRanger v2.0.1 (count)
Supplementary files format and content: H5, .csv, .tsv

source_name: mouse maternal-fetal interface

extract_protocol:
Isolation of cells from the implantation sites were done with enzymatic digestion using Liberase. For SMART-Seq2 processing, single cells were FACS sorted into 96 U-well plates into either trNK (NCR1+CD3ε-TCRb-CD19-CD45+CD122+CD49a+) or cNK (NCR1+CD3ε-TCRb-CD19-CD45+CD122+CD49b+) cells. For droplet-based scRNA-seq, total uNK cells (NCR1+CD3ε-TCRb-CD19-CD45+CD122+) were sorted into Eppendorf tubes.
RNA-Seq: SMART-Seq2 scRNA-seq libraries were prepared from trNK and cNK cells from gd9.5 maternal-fetal interface and sorted in 96 U-well plates. Libraries were prepared using Nextera XT DNA library preparation kit and sequenced using a NextSeq 500/550 High Output v2 kit 75 cycles (Illumina) on a Nextseq 500 (Illumina).
scRNA-Seq: For droplet-based scRNA-seq, 7,000 cells (sorted uNK or total unsorted cells) were loaded onto the Chromium Single Cell 3’ Chip A (10x Genomics) and processed through the chromium controller to generate Gel beads in Emulsion. RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics) as per the manufacturer’s instructions. Libraries were sequenced on an Illumina Hi-Seq.

value: mouse maternal-fetal interface

tag: sample id

tag: mouse id

tag: technology

value: droplet based (10x) scRNA-Seq

tag: atlas

value: maternal-fetal NK interface


title: NK_46.2e_KIRC5F_WTM : cellranger counts


title: ChAd-4_I-D7

first: Hye Kyung

last: Lee

tag: age

tag: gender

tag: vaccine

value: 1st dose, ChAdOx1

value: PBMCs


title: Healthy control_2

value: WT


title: Healthy control_1


title: ChAd-4_I-D4


title: NK_47.2d_WTF_C5M : cellranger counts


title: Genetically correction of Down syndrome_1


title: ChAd-3_I-D7


title: ChAd-6_I-D4


title: NK_45.3e_KIRF_C5M : cellranger counts


title: NK_17.3d_KIRF_C5M : cellranger counts


title: ChAd-3_I-D4


title: Adrenal_Glands_KO_ChIP_1

city: Montreal

first: Jiangping

last: Wu

address: 900 Rue Saint Denis

country: Canada

description: RPB1(NTD)-specific antibody ChIP DNA fragments

data_processing:
Base-calling was performed with RTA v3. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.  ChIP-seq reads were first trimmed for adapter sequences and low-quality score bases using Trimmomatic (Bolger et al., 2014). The resulting reads were mapped to the mouse reference genome (GRCm38) using BWA-MEM (Li and Durbin, 2009) in paired-end mode at default parameters. Only reads that had a unique alignment (mapping quality > 20) were retained, and PCR duplicates were marked using Picard tools. Peaks were called and annotated using MACS2 (Zhang et al., 2008) and HOMER (Heinz et al., 2010) software suites, respectively.
genes that lacked RPB1 ChIP-seq signal in the promoter region in the KO tissues were filtered out, as these genes were believed to have no signals in WT tissues neither.
Raw counts were normalized using edgeR’s TMM algorithm (Robinson et al., 2010) and were then transformed to log2 Counts Per Million (log2CPM) using the Voom function implemented in the Limma R package (Ritchie et al., 2015).
To construct the global metagene Pol II-binding profile, normalized read counts (Fragments Per Kilobase of transcript per Million Mapped reads (FPKM) of a full gene length plus 2,000-bp flanks (TSS - 2,000 bp to TES + 2,000 bp) were obtain from all the genes that passed the filtering. Both flanks were divided into 20 equal-sized bins of 100 bp each. The gene bodies were scaled to 60 bins for the full gene length. FPKM was calculated from BAM input files using ngs.plot (Shen et al., 2014) with the following parameters: -G mm10 -R genebody -D ensembl -FL 200 -BOX 0 -SE 1 -VLN 0 -LWD 2 -WD 9. These global metagene Pol II binding profiles were only for visualization of differences in  Pol II density, and customarily, and customarily, inferential statistics was not conducted for such profiling.
Genome_build: GRCm38
Supplementary_files_format_and_content: bigwig files contains the profile of ChIP-Seq. AG_TSS_counts_data.csv, AG_GENEBODY.counts_data.csv, AG_TES.counts_data.csv contain the raw counts of RPB1 signal In evry detected gene. AG_counts_data_tsv contains the raw counts of RPB1 signal in every gene. AG.log2cpm_data.tsv contains log2CPM value of RPB1 signal in every gene.

source_name: adrenal glands

extract_protocol:
The adrenal glands from 10-14-month old WT and KO female mice were resected and stored in liquid nitrogen immediately until use. Each gland was homogenized in 200 µl ice-cold PBS buffer with a handheld Polytron homogenizer. The final volume was brought to 1 ml with ice-cold PBS. The homogenized samples were crosslinked with 66.7 µl 16% formaldehyde (1% final) at room temperature for 15 minutes. They were quenched with 107 µl 1.25 M glycine (0.125 M final) at room temperature for another 10 minutes in rotating tubes. The samples were centrifuged, and the pellets were washed twice with ice-cold PBS. The crosslinked pellets were re-homogenized with the Polytron homogenizer and suspended in 300 µl swelling buffer (50 mM Tris (pH 8.0), 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and incubated on ice for 20 minutes to release nuclei. The nuclei were harvested by centrifugation, resuspended in 200 µl ChIP sonication buffer (10 mM Tris (pH 8.0), 1 mM EDTA, 0.5 mM EGTA, 0.5% SDS), and incubated on ice for 20 minutes. The nuclei were sonicated with a probe-based sonicator (FB120, probe:CL-18, FISHER SCIENTIFIC) at a 20% amplitude setting. The sonication was conducted using 15-second pulses at 15-second intervals for a total of 8 minutes. The sonicated nuclei were harvested by centrifugation, and then diluted with 800 µl ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris (pH 8.1), 167 mM NaCl) to reach the final SDS concentration of 0.1%. These samples represented sonicated chromatin ready for immunoprecipitation.  To quantify chromatin and assess the degree of its fragmentation, we treated 5% of the sonicated nuclei (50 µl/sample) with 10 µg of RNase A for 15 minutes at 37 ºC followed by 20 µg of proteinase K for 30 minutes at 65 ºC. They were de-crosslinked for 5 minutes at 95 ºC. DNA was extracted with the QIAquick PCR Purification Kit. DNA concentration was determined with a Nanodrop 1000 Fluorospectrometer. DNA fragment sizes were confirmed to be 200-800 bp in length, according to electrophoresis.  For immunoprecipitation, an equal amount of sonicated chromatin, based on their prior DNA measurements, of different samples was reacted with anti-RPB1 N-terminal domain Ab (D8L4Y) (1:100) at 4 ºC overnight, followed by 40-µl magnetic protein G beads (Bio-Rad) for another 2 hours at 4 ºC. The beads were rinsed with wash buffer (100 mM Tris (pH 8.0), 500 mM LiCl, 1% NP-40, 1% deoxycholic acid) for 5 times and then with TE buffer once. The chromatin was eluted with elution buffer (50 mM Tris (pH 8.0), 10 mM EDTA, 1% SDS) at 65 ºC for 10 minutes. The immunoprecipitated chromatins were de-crosslinked at 65 ºC overnight with NaCl adjusted to 200 mM. The chromatins were then treated with 10 ug RNase A/sample at 37 ºC for 1 hour, followed by 200 g proteinase K/sample for 2 hours at 45 ºC. DNA of the samples was purified with QIAquick PCR Purification kit and quantified by the Bioanalyzer (Agilient).
Libraries were prepared robotically with 0.2 to 2 ng of fragmented DNA ranging 100-300 bp in length, using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs), as per the manufacturer’s recommendations. Adapters and PCR primers were purchased from Integrated DNA Technologies . Size selection was carried out using SparQ beads (Qiagen) prior to PCR amplification (12 cycles). Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument. The libraries were normalized and pooled, and then denatured in 0.05 N NaOH and neutralized using HT1 buffer. The pool was loaded at 225 pM on an Illumina NovaSeq S4 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2 x 100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level. Each library was sequenced at 25 million reads.

value: adrenal glands

value: 129 sv X CD1

tag: Sex

value: female

tag: mouse number


title: Adrenal_Glands_WT_ChIP_3


title: ChAd-3_I-D0

city: Bethesda

address: 8 CENTER DR RM 107

value: Female


title: A71

city: Shenzhen

first: Fenglei

last: Chen

state: Guangdong Province

address: Futian District

department: orthopedics department

country: China

institute: The Eighth affilited Hospital of Sun-Yat-Sen University

data_processing:
Raw reads were treated with Trimmomatic tools(V0.36) to remove adapters.
Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15, drop reads which are less than 35% of initiation read length
Then reads quality was inspected using the FastQC software then output statistical result
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count and RPM values for each Sample

source_name: bone marrow derived

growth_protocol: bone marrow-derived mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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

treatment_protocol:
Osteogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with osteogenic differentiation medium
MSC were seeded in 12-well plates in osteogenic differentiation medium for 0 to 21 days. This medium was composed of DMEM containing 10% FBS, 0.1 μM dexamethasone, 10 mM β-glycerol phosphate, 50 μM ascorbic acid, 100 IU/ml penicillin, and 100 IU/ml streptomycin (Sigma). The medium was replaced every 3 days.

tag: cell line

value: bone marrow derived

value: mesenchymal stem cells

tag: treatment

value: osteogenic differentiation

tag: time

value: Day 14


title: Adrenal_Glands_WT_ChIP_2

tag: tissue


title: A69


title: NK_43.1h_WTF_C5M : cellranger counts


title: NK_46.4c_WTF_C5M : cellranger counts


title: A50


title: Adrenal_Glands_KO_3

data_processing:
Reads were trimmed from the 3' end to have a phred score of at least 30. Illumina sequencing adapters were removed from the reads, and all reads were required to have a length of at least 32 bp. Trimming and clipping were performed using Trimmomatic.
Upstream processing of FastQ files was performed as described previously (Bourgey et al., 2019), using the ENSEMBL GRCm38 (Mus musculus) release 97 mouse reference genome sequence and annotations. Each readset was aligned using STAR (Dobin et al., 2013), which creates a Binary Alignment Map file (.bam). Then, all readset BAM files from the same sample were merged into a single global BAM file using Picard.
The pairwise Pearson’s correlation values of samples were calculated. The correlation controlled the general transcripts expression consistency between samples. It could check sample mix-up or error in name assignment. Thus, samples belonging to the same design group/condition were expected to show a higher level of correlation.
Gene expression levels were quantified using StringTie. Specifically, the count matrix was extracted from StringTie output using the auxiliary script prepDE.py as provided on the StringTie website. A gene here could be a novel gene with no overlap with a known gene. This resulted in count data for StringTie-assembled gene models.
It is generally beneficial to filter out lowly expressed genes before exploratory data analysis, but importantly prior to differential expression analysis (to reduce the multiple testing burden). For this data set, we filtered out genes that do not exceed 1 CPM in at least three samples. Out of the original genes, 17,711 genes are left after filtering.  Each gene was tested for differential expression between WT and Armc5 KO adrenal glands with EdgeR Likely Ratio Tests. Due to the concern that the augmented Pol II pool caused by Armc5 deletion might generally affect the transcription of all the gene in the KO adrenal glands, we set normalization factors for each sample as the ratio between the log2CPM value of Rn7sk of the sample to the average of all log2CPM values of Rn7sk across all samples. Rn7sk was transcribed by Pol III and was thus independent of the putative influence of the Pol II pool size.
Genome_build: GRCm38
Supplementary_files_format_and_content: Bigwig files are ready to be viewed in Genome Viewer (UCSC).
Supplementary_files_format_and_content: Matrix csv file contains raw counts, log2CPM, 7sk RNA calibrated log2CPM of every gene and every sample

extract_protocol:
KO and WT adrenal glands were homogenized, and their total RNA was extracted by RNeasy kit (Qiagen).
The total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.), and its integrity was assessed on a 2100 Bioanalyzer (Agilent Technologies). rRNA was depleted from 250 ng of total RNA using QIAseq FastSelect (Human 96rxns). cDNA synthesis was achieved with the NEBNext RNA First-Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs), according to the manufacturer's instructions. Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). The average fragment size was determined using a LabChip GX (PerkinElmer). The libraries were normalized and pooled and then denatured in 0.05 N NaOH and neutralized using HT1 buffer. The pool was loaded at 225 pM on an Illumina NovaSeq S2 lane using the Xp protocol as per the manufacturer’s recommendations. The run was performed for 2 x 100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at a 1% level. Base-calling was performed with RTA v3. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.

tag: strain background

value: 30 weeks


title: ChAd-2_I-D4

institute: National Institutes of Health (NIH)


title: Adrenal_Glands_WT_ChIP_1

tag: strain

tag: genotype


title: Adrenal_Glands_KO_ChIP_3


title: A48

tag: cell type


title: ChAd-2_I-D7


title: Adrenal_Glands_KO_ChIP_2


title: NK_47.1k_KIRC5F_WTM : cellranger counts

tag: sample id


title: ChAd-4_I-D0


title: H54-2


title: Adrenal_Glands_KO_2


title: H49-1


title: ChAd-2_I-D0


title: Adrenal_Glands_KO_1


title: NK_43.1G_WTF_C5M : cellranger counts

tag: mouse id


title: H48-2


title: Adrenal_Glands_WT_3


title: Unsorted_16.2h_KIRC5F_WTM : cellranger counts

tag: technology

value: maternal-fetal interface


title: NK_47.1p_KIRF_C5M : cellranger counts

tag: atlas


title: H35-1


title: Unsorted_46.2e_KIRC5F_WTM : cellranger counts


title: ChAd-1_I-D2

tag: age

value: Male


title: Unsorted_17.3d_KIRF_C5M : cellranger counts

value: mouse maternal-fetal interface


title: BNT-52_II-D2

tag: gender

value: 2nd dose, BNT162b2


title: ChAd-1_I-D0

tag: vaccine


title: Unsorted_47.2d_WTF_C5M : cellranger counts

value: droplet based (10x) scRNA-Seq


title: BNT-52_II-D0


title: Adrenal_Glands_WT_1

tag: Sex


title: Liver, primary FLC, no treatment

city: Ithaca

first: Praveen

last: Sethupathy

address: T7 006D Veterinary Research Tower, Box 17

department: Biomedical Sciences

institute: Cornell University

library_source: genomic single cell

data_processing:
none provided by the submitter
Assembly: hg38
Supplementary files format and content: bam
Supplementary files format and content: tabix

source_name: Liver

extract_protocol: none provided by the submitter

value: Liver

tag: sample type

value: Chromatin

value: DP Fusion Detected

value: Nuclei isolated


title: Liver, primary FLC, collagenase treated

value: Nuclei isolated using collagenase


title: low-affinity ZF with clamp and without VP16, ZF ChIP DNA, replicate 2

first: Ahmad

middle: S

last: Khalil

address: 610 Commonwealth Avenue, Rm 405C

institute: Boston University

data_processing:
Adapter removal and 3′ quality trimming of paired-end reads were performed using cutadapt (Martin, 2011).
Reads were aligned using Bowtie2 (Langmead and Salzberg, 2012) to a combined genome consisting of S.pombe genome build ASM294v2 concatenated with S. cerevisiae genome build R64-2-1 (Engel et al., 2014) modified to include the Venus reporter at the URA3 locus.
Correctly paired uniquely mapping reads mapping to S. cerevisiae were selected using SAMtools (Li et al., 2009).
overage of fragments and fragment midpoints were generated using SAMtools (Li et al., 2009) and bedtools (Quinlan and Hall, 2010), and normalized to the number of S. pombe fragments in the library.
Transcription factor peak calling was performed for each strain by calling peaks in each replicate using MACS2 (Zhang et al., 2008), followed by filtering for reproducibility among replicates by the Irreproducible Discovery Rate (IDR) method (Li et al., 2011). The size of the small and large local regions used by MACS2 to model expected counts were set to 500 and 2000 bp, respectively, and the IDR threshold was set to 0.01.
For transcription factor ChIP-seq differential binding analysis, transcription factor peaks were called as described above. A non-redundant list of peaks called in the strains being compared was generated using bedtools (Quinlan and Hall, 2010), and the counts of fragment midpoints from both input and IP samples over these peaks were used as the input to a differential binding analysis with DESeq2 (Love et al., 2014), in which the linear model coefficient extracted represents the change in IP/input enrichment in the query strain versus the control strain.
Assembly: custom S. cerevisiae R64-2-1 modified with Venus reporter at URA3, S. pombe ASM294v2
Supplementary files format and content: BigWig of spike-in normalized fragment midpoint coverage.

organism: Saccharomyces cerevisiae

growth_protocol: 250 mL flasks of SDC were inoculated with overnight cultures and grown for 1 hour before induction with 100 nM B-estradiol, then grown for a further 8 hours to an OD600 of 0.525-0.625.

extract_protocol:
All cultures were diluted to OD600 0.525, then cells were crosslinked with 1% formaldehyde (from a 37% stock, Fisher) for 9 minutes at 30C with shaking. Fixation was quenched with a final concentrations of 125 mM glycine (EMD 4840 OmniPur) for 10 min at 30C with shaking. Cells were pelleted for 10 min at 4C at 3000 rpm (Haraeus Multifuge X3R), washed twice with ice-cold TE (Tris-HCl, EDTA), transferred to 4 bead-beater tubes/strain (orginally 250 mL culture) and frozen at -80C. Cell pellets were resuspended in 400 uL ice cold lysis buffer (50 mM HEPES, 140 mM NaCl, 1mM ethylenediaminetetraacetic acid, 1% Triton X-100, 0.1% Na-Deoxycholate, 1 mM phenylmythylsulfonyl fluoride, 200 uL Roche cOmplete protease inhibitors). 0.5 mm diameter glass beads were added to 1 mm below the meniscus. Cells were lysed by bead beating on a MagNA Lyser (Roche) three times for 45 s each at 4500 rpm with 2 min rests at 4C. Lysate was collected by puncturing the tube with a 21G needle and centrifugation at 2000 g for 2 min into a 2 mL microtube. The pellet was resuspended in lysis buffer, then sonicated for 6 pulses using a probe sonicator (Ngo Lab, Boston University) for 20 s at 25% amplitude with 2 min. intervening rests on ice, achieving a range of 150-1500 bp DNA fragments. Cell debris was pelleted by centrifiguation at max speed for 15 min at 4C. FLAG-tagged S.pombe generously shared by the Winston Lab (FWP567) was used as a spike-in control and was prepared similarly to the S.cerevisiae strains with a few modifications (grown in 250 mL YES media to OD600 0.65, split into 5 tubes, underwent 4 lysis steps on the bead beater and 5 sonication steps). The supernatant from the 4 preps of each strain (5 preps of S.pombe) were mixed together in a new low retention tube. To determine DNA concentration, 50 uL samples from each strain was isolated.  Samples were brought up to 200 uL with elution buffer, then incubated with 50 ug of RNAse A (Thermo Fisher Scientific) at 37C for 30 minutes to remove RNA.  Then 100 ug of Proteinase K (Thermo Fisher Scientific) was added and samples were incubated overnight (~16 hours) at 60C to degrade proteins and reverse crosslinks. Samples were then purified with the ChIP DNA Clean and Concentrator kit (Zymo Research), eluted with 100 uL water and concentrations were determined by Qubit 4 Fluorometer (Thermo Fisher Scientific). 50 uL were brought to 13.5 ng/uL concentration and split into 4 separate tubes, diluted to 1 mL lysis buffer. Input samples were concurrently isolated at 10% of the DNA concentration for the IP samples and brought to 100 uL lysis buffer. 1 ug anti-FLAG (Sigma F1804) were added to each IP sample. The prepared (lysed and sonicated) FLAG-tagged S.pombe chromatin was added as a spike-in control to 10% of the sample DNA concentration for all IP and input samples. Input samples were stored at 4C and IP samples rotated overnight at 4C. 30 uL Dynabeads Protein G (10004D, Thermo Fisher Scientific) per culture was added to a low retention tube and washed 3 times with 1 mL ice cold lysis buffer. Dynabeads were resuspended in 100 uL lysis buffer per culture. 100 uL of Dynabead solution was added to each antibody-pulldown sample and incubated at 4C for 4 hrs while rotating. Dynabeads were washed at room temperature on a magnet (twice with 1 mL lysis buffer, twice with 1 mL lysis buffer/500 mM NaCl, twice with 10 mM TrisHCl-pH8/250 mM LiCl/0.5% NP-40/0.5% sodium deoxycholate/1 mM EDTA, and once with 1 mL TE). Bound material was eluted by adding 200 uL of 50 mM Tris-HCl ph8/10 mM EDTA/1% SDS and incubating at 65C for 30 min. A second elution with the same buffer was combined with the first and tubes were incubated at 65C overnight to reverse crosslinks. Input samples were brought to 400 uL elution buffer and stored at 65C with antibody-pulldown samples. 50 ug of RNase A was added to each pulldown and input sample and incubated at 37C for 30 mins. 100 ug Proteinase K was added to each sample, then incubated at 55C for 4 hours.   DNA was purified with the ChIP Clean and Concentrator ChIP (4 preps/strain were concentrated into two preps in two columns) and eluted with 25 uL of water for IP samples/column (50 uL total) or 200 uL water for input samples and stored at -80C. Sample concentrations were measured with Qubit.
Illumina TruSeq ChIP

tag: group

tag: chip antibody

value: anti-FLAG (Sigma #1804)


title: low-affinity ZF with clamp and without VP16, ZF ChIP DNA, replicate 1


title: Unsorted_45.3e_KIRF_C5M : cellranger counts


title: low-affinity ZF without VP16, ZF ChIP DNA, replicate 2

value: low-affinity ZF without VP16


title: Liver, adjacent nonmalignant, no treatment

value: WT

tag: treatment


title: Liver, adjacent nonmalignant, collagenase treated

tag: tissue


title: Liver, metastatic FLC, no treatment


title: BNT-48_II-D3

value: Female

value: PBMCs


title: low-affinity ZF without VP16, ZF ChIP DNA, replicate 1


title: BNT-48_II-D0


title: Adrenal_Glands_WT_2

tag: strain background

value: 129 sv X CD1

value: female

value: adrenal glands


title: BNT-48_II-D7


title: Unsorted_47.1p_KIRF_C5M : cellranger counts

value: maternal-fetal interface


title: Liver, metastatic FLC, collagenase treated


title: Unsorted_43.1h_WTF_C5M : cellranger counts

value: mouse maternal-fetal interface


title: ZIP1

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

data_processing:
Alignment with BOWTIE2
Read count table generated with  FeatureCount
Supplementary_files_format_and_content: Read count

source_name: ATCC -> lab modified

growth_protocol: HL60 cells were purchased from American Type Culture Collection (ATCC, Manassas, VA) and maintained in Iscove's Modified Dulbecco's Medium (IMDM) (Gibco, Grand Island, NY) supplemented with 10% FBS (Fisher Scientific, Grand Island, NY).

extract_protocol:
total RNA using mirVana™ miRNA Isolation Kit Protocol (Ambion, Thermofisher Scientific, Waltham, MA)
Library construction was conducted on total RNA using the TruSeq Small RNA sample preparation kit (Illumina, San Diego, CA) and sequenced on an Illumina HiSeq 2500.

treatment_protocol: miRZip-378a-3p (ZIP) and scramble (SCR) pGreenPurTM lentivectors (Cat# CS970A-1, System Biosciences, Palo Alto, CA) encode either a miRZip hairpin interfering RNA designed to generate the full-length antisense miR-378a-3p or an empty vector, respectively. HL60 were seeded in 24-well plates and infected with a multiplicity of infection of 20 with ZIP or SCR using polybrene transduction reagent (8ug/mL) (Cat# TR-1003-G, Millipore, Burlington, MA) by spin transduction (1500g, 2 hours). Initial transduction efficiency was measured by flow cytometry on day 3. After puromycin (Cat# P8833; Sigma Aldrich; Burlington, MA) (2ug/mL) treatment on day 3 through day 8, selection efficiency was measured by flow cytometry.  Expression of the ZIP construct normalized to U6 was confirmed by real time polymerase chain reaction (qPCR) using QuantiMirTM (Cat#RA420A-hU6, System Biosciences), using the ABI 7300 Real Time PCR System (Applied Biosystem, Foster City, CA).  Expression of miR-378-3p normalized to U6 was assessed by qPCR using TaqManTM MicroRNA Assays (Cat# 4427975, Applied Biosystems). Presence of green fluorescent protein (GFP) in both ZIP and SCR vectors was confirmed by polymerase chain reaction (PCR) and fluorescent microscopy (Nikon Eclipse TE2000-S Inverted microscope, Melville, NY).

tag: cell line

value: Transduced with mirZIP-378-3p vector


title: high-affinity ZF without VP16, ZF ChIP DNA, replicate 2

value: high-affinity ZF without VP16

tag: strain


title: Unsorted_47.1k_KIRC5F_WTM : cellranger counts

tag: genotype

value: droplet based (10x) scRNA-Seq


title: ChAd-1_I-D7

value: Male

value: 1st dose, ChAdOx1

tag: cell type


title: E6.43_CD19IgM_rep3

description:
E6.43_B_1HSC_rep3
monoclonal sample derived from single HSC

data_processing:
Reference preparation: imputed parental genomes were prepared (“pseudogenomes” (Crowley et al., 2015; Zou et al., 2014)) for each organism, using a custom script (all custom software tools mentioned are available on https://github.com/gimelbrantlab/ASEReadCounter_star); VCF file with one allele considered as a reference (maternal C57BL/6 or first phased allele) and the other as an alternative allele. Only heterozygous sites were used.
Alignment: RNA-seq reads were trimmed from nextera adapters with cutadapt v.1.14 using the wrapper trim_galore; reads were then aligned with STAR aligner v.2.5.4a (Dobin et al., 2013) on each of two pseudogenomes, with default threshold on quality of alignment. Only uniquely alligned reads were used.
Allele assigment. Given vcf file with heterozygous positions, coverage over each SNP was calculated using custom script based on samtools mpileup and parsed to obtain the table with allelic counts. Data processing steps from read alignment to allelic counts were based on a modification of the GATK pipeline (Castel et al., 2015), and described in: https://github.com/gimelbrantlab/ASEReadCounter_star
Allele counting per gene. All exons belonging to the same gene were merged into a single gene model based on GTF file (RefSeq GTF file, GRCm38.68, was downloaded from Ensemble ftp://ftp.ensembl.org/pub/release-68/gtf/ (Zerbino et al., 2018)), excluding overlapping regions that belong to multiple genes. This step was based on the GATK pipeline (Castel et al., 2015).
AI point estimate per gene obtained as a proportion of maternal gene counts to total allelic gene counts
RNA abundance: counts were obtained with featureCountstool from the subread v.2.0.0 package, using the same bam files processed during ASE analysis as described (previous to counts, alignments were performed on inputed parental genomes, then merged into one file, which was used as such to count reads with featureCounts); abundance was measured using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: allelic counts, allelic imbalance with confidence intervals, cpm (counts per million) values for RNA abundance

extract_protocol:
RNA was isolated from sorted cells using Trizol reagent or Absolutely RNA Nanoprep Kit (Agilent #400753)  according to the manufacturer`s protocol.
10 nanogram RNA samples were used to prepare sequencing libraries with SMART-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories, Inc., California, USA) according to the manufacturer`s protocol.

value: C57BL/6 x CAST/EiJ F11

tag: cells

tag: rna extraction

value: Trizol

tag: number of cells sorted for rna isolation

tag: library replicate

tag: donor animal

value: donor animal #6

tag: recipient animal

value: recipient animal #6.43


title: BNT-39_II-D7

tag: age

tag: gender

tag: vaccine

value: 2nd dose, BNT162b2


title: Unsorted_46.4c_WTF_C5M : cellranger counts

tag: sample id

tag: mouse id

tag: technology

tag: atlas


title: ZIP2

tag: cell line

tag: treatment


title: reporter-only, ZF ChIP DNA, replicate 4

tag: group

value: reporter-only

tag: strain

tag: chip antibody

value: anti-FLAG (Sigma #1804)


title: SCR1

value: Transduced with empty vector


title: UNT

source_name: ATCC

value: untransduced


title: BNT-38_II-D7

value: Female

tag: cell type

value: PBMCs


title: low-affinity ZF with clamp, ZF ChIP DNA, replicate 2

value: low-affinity ZF with clamp


title: BNT-39_II-D2


title: SCR2


title: E6.43_CD19IgM_rep1

description:
E6.43_B_1HSC_rep1
monoclonal sample derived from single HSC

value: C57BL/6 x CAST/EiJ F9

tag: cells

tag: rna extraction

tag: number of cells sorted for rna isolation

tag: Sex

value: female


title: BNT-38_II-D0

tag: age


title: E6.43_CD19IgM_rep2

description:
E6.43_B_1HSC_rep2
monoclonal sample derived from single HSC

value: C57BL/6 x CAST/EiJ F10

tag: library replicate

tag: donor animal

tag: recipient animal


title: low-affinity ZF, ZF ChIP DNA, replicate 2

value: low-affinity ZF


title: high-affinity ZF without VP16, ZF ChIP DNA, replicate 1

value: high-affinity ZF without VP16


title: reporter-only, ZF ChIP DNA, replicate 3


title: BNT-36_II-D10

tag: gender

tag: vaccine


title: E6.42_CD19IgM_rep2

description:
E6.42_B_1HSC_rep2
monoclonal sample derived from single HSC, not processed (QC no pass)

value: C57BL/6 x CAST/EiJ F7

value: recipient animal #6.42


title: S121_grade3_chondrosarcoma

city: Norwich

first: Darrell

last: Green

address: Earlham Road

department: Norwich Medical School

institute: University of East Anglia

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapter and HD signatures [Sorefan et al 2012] were trimmed and the files were converted from redundant to non-redundant format
the reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change on confidence intervals built on replicates, offset = 20
Genome_build: GRCh38
Supplementary_files_format_and_content: csv, raw abundances

source_name: chondrosarcoma

extract_protocol:
Resected tissue was used for total RNA extraction before construction of small RNA libraries with HD adapters.
Illumina compatible method with HD adapters

tag: tissue

value: chondrosarcoma

tag: grade


title: low-affinity ZF, ZF ChIP DNA, replicate 1


title: E6.42_CD19IgM_rep1

description:
E6.42_B_1HSC_rep1
monoclonal sample derived from single HSC

value: C57BL/6 x CAST/EiJ F6

value: Trizol

value: donor animal #6


title: E6.42_CD19IgM_rep3

description:
E6.42_B_1HSC_rep3
monoclonal sample derived from single HSC

value: C57BL/6 x CAST/EiJ F8


title: S110_grade3_chondrosarcoma


title: S116_grade3_chondrosarcoma


title: BNT-39_II-D0

source_name: PBMCs

value: 2nd dose, BNT162b2


title: BNT-38_II-D2


title: high-affinity ZF, ZF ChIP DNA, replicate 2

value: high-affinity ZF

value: anti-FLAG (Sigma #1804)


title: E6.2_CD19IgM_rep3

description:
E6.2_B_50HSCs_rep3
polyclonal sample derived from 50 HSCs

value: C57BL/6 x CAST/EiJ F5

value: recipient animal #6.2


title: low-affinity ZF with clamp, ZF ChIP DNA, replicate 1

value: low-affinity ZF with clamp


title: BNT-36_II-D0

value: Female

value: PBMCs


title: E6.2_CD19IgM_rep2

description:
E6.2_B_50HSCs_rep2
polyclonal sample derived from 50 HSCs

value: C57BL/6 x CAST/EiJ F4

value: female


title: S63_grade3_chondrosarcoma


title: S126_grade2_chondrosarcoma


title: BNT-36_II-D3


title: BNT-27_II-D3


title: E6.1_CD19IgM_rep3

description:
E6.1_B_50HSCs_rep3
polyclonal sample derived from 50 HSCs

value: C57BL/6 x CAST/EiJ F2

value: recipient animal #6.1


title: reporter-only, ZF ChIP DNA, replicate 1

value: reporter-only


title: low-affinity ZF with clamp and without VP16, input DNA, replicate 2


title: E6.1_CD19IgM_rep2

description:
E6.1_B_50HSCs_rep2
polyclonal sample derived from 50 HSCs

value: C57BL/6 x CAST/EiJ F1


title: S98_grade2_chondrosarcoma

value: chondrosarcoma


title: S102_grade2_chondrosarcoma


title: reporter-only, ZF ChIP DNA, replicate 2


title: BNT-27_II-D0


title: S132_grade1_chondrosarcoma


title: S131_grade1_chondrosarcoma


title: BNT-25_II-D7


title: S127_grade1_chondrosarcoma


title: low-affinity ZF without VP16, input DNA, replicate 1

value: low-affinity ZF without VP16


title: BNT-26_II-D4


title: E13.29_CD19IgM_rep2

description:
E13.29_B_1HSC_rep2
monoclonal sample derived from single HSC

value: Trizol

value: donor animal #13

value: recipient animal #13.29


title: BNT-27_II-D7

value: 2nd dose, BNT162b2


title: S95_grade1_chondrosarcoma


title: E6.2_CD19IgM_rep1

description:
E6.2_B_50HSCs_rep1
polyclonal sample derived from 50 HSCs

value: C57BL/6 x CAST/EiJ F3

value: donor animal #6


title: low-affinity ZF with clamp and without VP16, input DNA, replicate 1


title: E15.10_CD19IgM_rep2

description:
E15.10_B_1HSC_rep2
monoclonal sample derived from single HSC

value: donor animal #15

value: recipient animal #15.10


title: BNT-26_II-D0

value: Female

value: PBMCs


title: high-affinity ZF, ZF ChIP DNA, replicate 1

value: high-affinity ZF

value: anti-FLAG (Sigma #1804)


title: reporter-only, input DNA, replicate 4


title: E13.24_CD19IgM_rep3

description:
E13.24_B_1HSC_rep3
monoclonal sample derived from single HSC

value: female

value: recipient animal #13.24


title: high-affinity ZF without VP16, input DNA, replicate 2

value: high-affinity ZF without VP16


title: E15.10_CD19IgM_rep1

description:
E15.10_B_1HSC_rep1
monoclonal sample derived from single HSC

value: C57BL/6 x CAST/EiJ F1


title: S89_grade1_chondrosarcoma

value: chondrosarcoma


title: E13.29_CD19IgM_rep1

description:
E13.29_B_1HSC_rep1
monoclonal sample derived from single HSC

value: Trizol


title: BNT-25_II-D0


title: BNT-26_II-D8


title: S105_grade1_chondrosarcoma


title: S92_clearCellChondrosarcoma

tag: tissue type

value: clear cell


title: E13.24_CD19IgM_rep2

description:
E13.24_B_1HSC_rep2
monoclonal sample derived from single HSC

value: donor animal #13


title: BNT-24_II-D9

value: 2nd dose, BNT162b2


title: low-affinity ZF without VP16, input DNA, replicate 2

tag: group

value: low-affinity ZF without VP16


title: E6.1_CD19IgM_rep1

description:
E6.1_B_50HSCs_rep1
polyclonal sample derived from 50 HSCs, not processed (QC no pass)

tag: strain

value: donor animal #6

value: recipient animal #6.1


title: reporter-only, input DNA, replicate 3

value: reporter-only

tag: chip antibody


title: BNT-25_II-D1

value: Female

tag: cell type


title: BNT-24_II-D2

value: PBMCs


title: S60_normalCartilage

source_name: cartilage

value: cartilage

value: normal


title: high-affinity ZF without VP16, input DNA, replicate 1


title: E13.24_CD19IgM_rep1

description:
E13.24_B_1HSC_rep1
monoclonal sample derived from single HSC, not processed (QC no pass)

tag: cells

value: female


title: S87_normalCartilage


title: low-affinity ZF with clamp, input DNA, replicate 1

value: low-affinity ZF with clamp


title: low-affinity ZF with clamp, input DNA, replicate 2


title: BNT-23_II-D7


title: E15.2_CD19IgM_rep2

description:
E15.2_B_200HSCs_rep2
polyclonal sample derived from 200 HSCs

tag: rna extraction

value: Absolutely RNA Nanoprep Kit

value: donor animal #15

value: recipient animal #15.2


title: S58_normalCartilage


title: E15.2_CD19IgM_rep1

description:
E15.2_B_200HSCs_rep1
polyclonal sample derived from 200 HSCs

value: C57BL/6 x CAST/EiJ F1

tag: number of cells sorted for rna isolation


title: S55_normalCartilage


title: low-affinity ZF, input DNA, replicate 2

value: low-affinity ZF


title: BNT-23_II-D4


title: low-affinity ZF, input DNA, replicate 1


title: E13.2_CD19IgM_rep2

description:
E13.2_B_200HSCs_rep2
polyclonal sample derived from 200 HSCs

value: Trizol

tag: Sex

value: donor animal #13

value: recipient animal #13.2


title: E13.2_CD19IgM_rep1

description:
E13.2_B_200HSCs_rep1
polyclonal sample derived from 200 HSCs


title: S53_normalCartilage


title: S50_normalCartilage


title: high-affinity ZF, input DNA, replicate 2

value: high-affinity ZF


title: BNT-17_II-D7

tag: age

value: 2nd dose, BNT162b2


title: BNT-17_II-D0


title: reporter-only, input DNA, replicate 2

value: reporter-only


title: E13.1_CD19IgM_rep2

description:
E13.1_B_200HSCs_rep2
polyclonal sample derived from 200 HSCs

tag: library replicate

value: recipient animal #13.1


title: BNT-24_II-D0

value: Female

value: PBMCs


title: BNT-17_II-D3


title: reporter-only, input DNA, replicate 1


title: BNT-13_II-D7


title: BNT-13_II-D4


title: BNT-23_II-D0


title: control_CD19IgM_rep4

description:
non-clonal_B_rep4
non-clonal sample isolated directly from donor mouse without transplantation

tag: donor animal

value: donor animal #17


title: E13.1_CD19IgM_rep1

description:
E13.1_B_200HSCs_rep1
polyclonal sample derived from 200 HSCs

value: female

tag: recipient animal


title: control_CD19IgM_rep3

description:
non-clonal_B_rep3
non-clonal sample isolated directly from donor mouse without transplantation


title: control_CD19IgM_rep2

description:
non-clonal_B_rep2
non-clonal sample isolated directly from donor mouse without transplantation, not processed (QC no pass)


title: BNT-13_II-D0

tag: gender


title: high-affinity ZF, input DNA, replicate 1


title: RnGFP_wing_ChIP_rep2_input

city: New York

first: Ryan

last: Loker

address: 3227 Broadway

institute: Columbia University

data_processing:
Reads taken from multiplexed Next-seq run were trimmed using the standard Basespace flowthrough (Bcl2Fastq) on pre-defined indices
RNA-seq raw count files generated by Rsubread FeatureCounts. GTF file; dm6.ensGene.gtf.gz, ignoreDup = FALSE, countMultiMappingReads = FALSE, GTF.featureType = "exon"
Bigwig files generated from BAM files using Deeptools (bamCoverage) and normalized to genome coverage - RPGC (ATAC-seq).
For ATAC Bowtie2 was used to map reads to Drosophila melanogaster genome (dm6) using default parameters with paired-end options (ATAC-seq).
For RNA-seq HISAT2 was used to map reads to the Drosophila melanogaster genome (dm6) with default parameters
Assembly: dm6
Supplementary files format and content: bigwig files generated from BAM files using Deeptools (bamCoverage) and normalized to genome coverage - RPGC (ATAC-seq) or RPKM (ChIP-seq)

source_name: L3 imaginal disc

growth_protocol: Drosophila larvae were raised on standard cornmeal food and kept at 25 degrees untill the wandering 3rd instar stage before harvesting of imaginal discs.

extract_protocol:
Imaginal discs of 3rd instar larvae were dissected in PBS on ice.
ChIP-seq library constructed using NEBnext Ultra II DNA library prep kit for Illumina

value: Wing imaginal disc

tag: genotype

value: rn-GFP


title: RnGFP_wing_ChIP_rep2

tag: tissue

value: Abcam ab290


title: RnGFP_wing_ChIP_rep1


title: RnGFP_wing_ChIP_rep1_input


title: BNT-9_II-D7

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Trimmed RNA-seq data were aligned to the human V, D and J genes and obtained immune clonotypes using MiXCR (Bolotin et al., Nat Methods, 2015; Bolotin et al., Nat Biotechnol, 2017).
Assembly: hg19
Supplementary files format and content: HTSeq counts from RNA-seq samples

tag: vaccine


title: BNT-9_II-D4


title: control_CD19IgM_rep1

description:
non-clonal_B_rep1
non-clonal sample isolated directly from donor mouse without transplantation, not processed (QC no pass)


title: E13.29_CD4CD8_rep2

description:
E13.29_T_1HSC_rep2
monoclonal sample derived from single HSC

value: recipient animal #13.29


title: BNT-9_II-D0


title: RNA_wing_nub1_rep3

extract_protocol:
Imaginal discs of 3rd instar larvae were dissected in PBS on ice.
RNA-seq library constructed using NEBnext Ultra II directional RNA library prep kit for Illumina


title: E13.29_CD4CD8_rep1

description:
E13.29_T_1HSC_rep1
monoclonal sample derived from single HSC

value: C57BL/6 x CAST/EiJ F1


title: RNA_wing_nub1_rep2


title: E13.24_CD4CD8_rep2

description:
E13.24_T_1HSC_rep2
monoclonal sample derived from single HSC

value: recipient animal #13.24


title: E13.24_CD4CD8_rep1

description:
E13.24_T_1HSC_rep1
monoclonal sample derived from single HSC

value: Trizol


title: RNA_wing_nub1_rep1