title: after MTX rep16

description:
Gene expression 3 months after  methotrexate treatment from a rheumatoid arthritis patient
C95.3T

source_name: CD4+ T cells after methotrexate treatment rep16


title: 4_7H_UcNK_A282_H6_S282 : 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: filtered out of SS2 NK atlas


title: 9_5B_UtrNK_A266_G2_S266 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: after MTX rep15

type: RNA

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

country: Japan

institute: Chiba University

description:
Gene expression 3 months after  methotrexate treatment from a rheumatoid arthritis patient
C93.3T

hyb_protocol: Agilent one-color Quick Amp Labeling Kit protocol

scan_protocol: Agilent one-color gene expression hyb/wash protocol

data_processing: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution.

organism: Homo sapiens

source_name: CD4+ T cells after methotrexate treatment rep15

label_protocol: DNA microarray anasysis was performed using a Quick Amp labeling kit.

extract_protocol: PBMCs were isolated using Ficoll-Paque Premium 1.073. CD4+ T cells were further purified uisng Human CD4+ T cell isolation kit (Milutenyi). RNA was prepared using the RNeasy Mini Kit (QIAGEN) following the manufacturer's recommendations.

tag: individual

tag: disease state

value: rheumatoid arthritis patient

tag: treatment

value: 3 months after  methotrexate

tag: cell type

value: CD4+ T cells


title: after MTX rep25

description:
Gene expression 3 months after  methotrexate treatment from a rheumatoid arthritis patient
C115.3T

source_name: CD4+ T cells after methotrexate treatment rep25


title: 15_4G_UtrNK_A184_H4_S184 : SS2 sample


title: 11_1i_UcNK_A9_A9_S9 : SS2 sample


title: after MTX rep12

description:
Gene expression 3 months after  methotrexate treatment from a rheumatoid arthritis patient
C87.3T

source_name: CD4+ T cells after methotrexate treatment rep12


title: 9_5B_UcNK_A52_E4_S52 : SS2 sample


title: after MTX rep10

description:
Gene expression 3 months after  methotrexate treatment from a rheumatoid arthritis patient
C80.3T

source_name: CD4+ T cells after methotrexate treatment rep10


title: after MTX rep6

description:
Gene expression 3 months after  methotrexate treatment from a rheumatoid arthritis patient
C19.3T

source_name: CD4+ T cells after methotrexate treatment rep6


title: after MTX rep11

description:
Gene expression 3 months after  methotrexate treatment from a rheumatoid arthritis patient
C85.3T

source_name: CD4+ T cells after methotrexate treatment rep11


title: after MTX rep8

description:
Gene expression 3 months after  methotrexate treatment from a rheumatoid arthritis patient
C49.3T

source_name: CD4+ T cells after methotrexate treatment rep8


title: after MTX rep9

description:
Gene expression 3 months after  methotrexate treatment from a rheumatoid arthritis patient
C71.3T

source_name: CD4+ T cells after methotrexate treatment rep9


title: after MTX rep5

description:
Gene expression 3 months after  methotrexate treatment from a rheumatoid arthritis patient
C16.3T

source_name: CD4+ T cells after methotrexate treatment rep5


title: after MTX rep3

description:
Gene expression 3 months after  methotrexate treatment from a rheumatoid arthritis patient
A34.3T

source_name: CD4+ T cells after methotrexate treatment rep3


title: 11_3E_UcNK_A167_F11_S167 : SS2 sample


title: after MTX rep7

description:
Gene expression 3 months after  methotrexate treatment from a rheumatoid arthritis patient
C43.3T

source_name: CD4+ T cells after methotrexate treatment rep7


title: after MTX rep4

description:
Gene expression 3 months after  methotrexate treatment from a rheumatoid arthritis patient
C14.3T

source_name: CD4+ T cells after methotrexate treatment rep4


title: 15_4G_UtrNK_A186_H6_S186 : SS2 sample


title: 8_1D_UcNK_A287_H11_S287 : SS2 sample


title: 4_7H_UtrNK_A59_E11_S59 : SS2 sample


title: after MTX rep1

description:
Gene expression 3 months after  methotrexate treatment from a rheumatoid arthritis patient
A29.3T

source_name: CD4+ T cells after methotrexate treatment rep1


title: 11_1i_UtrNK_A323_C11_S323 : SS2 sample


title: 11_1i_UtrNK_A316_C4_S316 : SS2 sample


title: 9_5B_UcNK_A40_D4_S40 : SS2 sample


title: 15_4G_UcNK_A357_F9_S357 : SS2 sample


title: after MTX rep2

description:
Gene expression 3 months after  methotrexate treatment from a rheumatoid arthritis patient
A30.3T

source_name: CD4+ T cells after methotrexate treatment rep2


title: 9_5B_UtrNK_A197_A5_S197 : SS2 sample


title: 8_1D_UcNK_A227_C11_S227 : SS2 sample


title: 4_7H_UtrNK_A52_E4_S52 : SS2 sample


title: before MTX rep27

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C117.0T

source_name: CD4+ T cells before methotrexate treatment rep27

value: before methotrexate


title: before MTX rep23

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C109.0T

source_name: CD4+ T cells before methotrexate treatment rep23


title: before MTX rep26

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C116.0T

source_name: CD4+ T cells before methotrexate treatment rep26


title: before MTX rep25

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C115.0T

source_name: CD4+ T cells before methotrexate treatment rep25


title: before MTX rep28

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
K20.0T

source_name: CD4+ T cells before methotrexate treatment rep28


title: before MTX rep24

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C111.0T

source_name: CD4+ T cells before methotrexate treatment rep24


title: 4_7H_UcNK_A257_F5_S257 : SS2 sample

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

source_name: mouse maternal-fetal interface


title: 9_3G_UtrNK_A178_G10_S178 : SS2 sample


title: before MTX rep22

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C108.0T

source_name: CD4+ T cells before methotrexate treatment rep22


title: 4_7H_UcNK_A226_C10_S226 : SS2 sample


title: before MTX rep20

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C103.0T

source_name: CD4+ T cells before methotrexate treatment rep20


title: 9_5B_UcNK_A8_A8_S8 : SS2 sample


title: 15_4G_UcNK_A361_G1_S361 : SS2 sample


title: 11_1i_UtrNK_A307_B7_S307 : SS2 sample


title: 11_3E_UcNK_A111_B3_S111 : SS2 sample


title: 8_1D_UcNK_A242_E2_S242 : SS2 sample


title: 4_7H_UcNK_A264_F12_S264 : SS2 sample


title: before MTX rep19

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C102.0T

source_name: CD4+ T cells before methotrexate treatment rep19


title: 15_4G_UtrNK_A121_C1_S121 : SS2 sample


title: before MTX rep17

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C96.0T

source_name: CD4+ T cells before methotrexate treatment rep17


title: before MTX rep16

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C95.0T

source_name: CD4+ T cells before methotrexate treatment rep16


title: 11_3E_UtrNK_A244_E4_S244 : SS2 sample


title: 4_7H_UcNK_A267_G3_S267 : SS2 sample


title: 9_5B_UtrNK_A220_C4_S220 : SS2 sample


title: before MTX rep15

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C93.0T

source_name: CD4+ T cells before methotrexate treatment rep15


title: 4_7H_UcNK_A253_F1_S253 : SS2 sample


title: before MTX rep12

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C87.0T

source_name: CD4+ T cells before methotrexate treatment rep12


title: before MTX rep11

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C85.0T

source_name: CD4+ T cells before methotrexate treatment rep11


title: before MTX rep21

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C107.0T

source_name: CD4+ T cells before methotrexate treatment rep21


title: 9_3G_UtrNK_A165_F9_S165 : SS2 sample


title: before MTX rep10

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C80.0T

source_name: CD4+ T cells before methotrexate treatment rep10


title: before MTX rep18

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C100.0T

source_name: CD4+ T cells before methotrexate treatment rep18


title: before MTX rep14

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C92.0T

source_name: CD4+ T cells before methotrexate treatment rep14


title: before MTX rep13

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C91.0T

source_name: CD4+ T cells before methotrexate treatment rep13


title: before MTX rep8

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C49.0T

source_name: CD4+ T cells before methotrexate treatment rep8


title: 15_4G_UtrNK_A176_G8_S176 : SS2 sample


title: 11_1i_UtrNK_A338_E2_S338 : SS2 sample


title: before MTX rep9

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C71.0T

source_name: CD4+ T cells before methotrexate treatment rep9


title: 8_1D_UcNK_A249_E9_S249 : SS2 sample


title: before MTX rep7

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C43.0T

source_name: CD4+ T cells before methotrexate treatment rep7


title: before MTX rep6

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C19.0T

source_name: CD4+ T cells before methotrexate treatment rep6


title: 9_5B_UcNK_A6_A6_S6 : SS2 sample

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

source_name: mouse maternal-fetal interface


title: 8_1D_UtrNK_A91_H7_S91 : SS2 sample


title: Piezo1&2_silenced_rep4 [si-P1+2_rep4]

city: Malmö

first: Lena

last: Eliasson

address: Jan Waldenströms gata 35

country: Sweden

institute: Lund University Diabetes Centre

library_source: transcriptomic

data_processing:
Quality control of the fastq files was performed with FastQC (v0.11.8) and MultiQC (v1.7)
Reads were mapped to the transcriptome and quantified by Salmon (v.0.14.0)
Genreration of normalized gene-sumarized transctipt counts and differential gene expression analysis was performed using DESeq2 (v1.25.10).
Genome_build: Rnor 6.0
Supplementary_files_format_and_content: Normalized transcript counts for every gene and every sample  by Deseq2

organism: Rattus norvegicus

growth_protocol: INS-1 832/13 cells were cultured in RPMI 1640 (HyClone) medium containing 11.1 mΜ D-glucose (Sigma) supplemented with 10% fetal bovine serum (Sigma), 10 mM HEPES (HyClone), 100 U/ml penicillin (HyClone), 100 μg/ml streptomycin (HyClone), 2 mM L-glutamine (HyClone), 1 mM sodium pyruvate (HyClone) and 0.05 mΜ 2-mercaptoethanol (Sigma), at 37°C in a humidified atmosphere containing 95% air and 5% CO2

extract_protocol:
Total mRNA was extracted from the transfected cells using the RNeasy® plus Mini kit (Qiagen) following the manufacturers’ instructions.
Libraries were prepared using TruSeq Stranded  mRNA Library Prep Kit (#20020594, Illumina) and sequenced with NextSeq® 500/550 High Output Kit v2.5 (#20024907, Illumina)

treatment_protocol: INS-1 832/13 cells were seeded by 150,000 per well in 24 well plates in penicillin/streptomycin-free culture medium prior to transfection the next day. Rat ON-TARGET plus smart-pool Piezo1 (#L-093854-02-0005, Dharmacon) or Piezo2 (#L-092136-02-0005, Dharmacon) RNA interference oligonucleotides (final concentration: 25 nM) were used to silence Piezo1 or Piezo2 and ON-TARGET plus negative control (#D-001810-10-20, Dharmacon) was served as a control. The siRNA was transfected using Lipofectamin® RNAimax (#13778150, Thermofisher Scientific). Double transfection with the same protocol was performed after 48h and maintained for another 48h for later measurements.

tag: cell line


title: before MTX rep5

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C16.0T

source_name: CD4+ T cells before methotrexate treatment rep5


title: Piezo1&2_silenced_rep2 [si-P1+2_rep2]


title: 11_1i_UtrNK_A374_H2_S374 : SS2 sample


title: before MTX rep3

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
A34.0T

source_name: CD4+ T cells before methotrexate treatment rep3


title: before MTX rep4

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
C14.0T

source_name: CD4+ T cells before methotrexate treatment rep4


title: 8_1D_UtrNK_A69_F9_S69 : SS2 sample


title: before MTX rep2

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
A30.0T

source_name: CD4+ T cells before methotrexate treatment rep2


title: 11_3E_UtrNK_A242_E2_S242 : SS2 sample


title: Piezo1&2_silenced_rep3 [si-P1+2_rep3]


title: 9_5B_UtrNK_A195_A3_S195 : SS2 sample


title: 9_5B_UtrNK_A244_E4_S244 : SS2 sample


title: 9_5B_UcNK_S3 : SS2 sample


title: 11_3E_UtrNK_A277_H1_S277 : SS2 sample


title: 4_7H_UtrNK_A12_A12_S12 : SS2 sample


title: Piezo2_silenced_rep4 [si-P2_rep4]


title: Piezo2_silenced_rep3 [si-P2_rep3]


title: Piezo1&2_silenced_rep1 [si-P1+2_rep1]


title: 15_4G_UcNK_A315_C3_S315 : SS2 sample


title: 9_5B_UtrNK_A267_G3_S267 : SS2 sample


title: Piezo2_silenced_rep2 [si-P2_rep2]


title: Piezo2_silenced_rep1 [si-P2_rep1]


title: 4_7H_UtrNK_A49_E1_S49 : SS2 sample


title: leaf_Wild-type_rep2

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: Gene expression of Arabidopsis leaves of wild type

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of AraGene-1_0-st type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis leaves

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Plants were grown for 6 weeks on soil under short day conditions (8.5 h day, light intensity: 70 - 100 µmol m-2 s-1, day temperature: 22 °C, night temperature: 18 °C, relative humidity: 50-60%).

extract_protocol: Total leaf RNA was extracted with the peqGOLD Total RNA Kit (peqlab) according to the manufacturer's instructions followed by DNA digestion with the DNase I Digest Kit (VWR).

treatment_protocol: no treatment

tag: genoytpe

value: Wild type

value: leaf

tag: age

value: 6 weeks


title: 15_4G_UcNK_A358_F10_S358 : SS2 sample


title: leaf_Wild-type_rep3


title: 11_1i_UcNK_A38_D2_S38 : SS2 sample


title: leaf_Wild-type_rep4


title: before MTX rep1

description:
Gene expression before methotrexate treatment from a rheumatoid arthritis patient
A29.0T

source_name: CD4+ T cells before methotrexate treatment rep1


title: 8_1D_UtrNK_A33_C9_S33 : SS2 sample


title: 15_4G_UtrNK_A168_F12_S168 : SS2 sample


title: Piezo1_silenced_rep4 [si-P1_rep4]


title: 9_3G_UcNK_A347_E11_S347 : SS2 sample


title: 11_1i_UcNK_A91_H7_S91 : SS2 sample


title: Piezo1_silenced_rep3 [si-P1_rep3]


title: 15_4G_UtrNK_A155_E11_S155 : SS2 sample


title: 11_3E_UcNK_A144_D12_S144 : SS2 sample


title: 15_4G_UcNK_A344_E8_S344 : SS2 sample


title: 15_4G_UcNK_A334_D10_S334 : SS2 sample


title: leaf_Wild-type_rep1


title: leaf_HYPK-knockout_exon2_rep3

description: Gene expression of Arabidopsis leaves of knockout of HYPK by T-DNA insertion in the second exon


title: Piezo1_silenced_rep2 [si-P1_rep2]


title: 9_5B_UcNK_A93_H9_S93 : SS2 sample


title: leaf_HYPK-knockout_exon2_rep1

value: knockout of HYPK by T-DNA insertion in the second exon


title: leaf_HYPK-knockout_exon2_rep2


title: 8_1D_UcNK_A286_H10_S286 : SS2 sample


title: Piezo1_silenced_rep1 [si-P1_rep1]


title: scramble_siRNA_rep4 [si-Ctrl_rep4]

value: non-targeting siRNA treated


title: scramble_siRNA_rep2 [si-Ctrl_rep2]


title: leaf_HYPK-knockout_exon1_rep3

description: Gene expression of Arabidopsis leaves of knockout of HYPK by T-DNA insertion in the first exon


title: scramble_siRNA_rep3 [si-Ctrl_rep3]


title: 9_3G_UcNK_A375_H3_S375 : SS2 sample


title: 4_7H_UcNK_A240_D12_S240 : SS2 sample


title: leaf_HYPK-knockout_exon1_rep4

value: knockout of HYPK by T-DNA insertion in the first exon


title: 9_3G_UtrNK_A171_G3_S171 : SS2 sample


title: scramble_siRNA_rep1 [si-Ctrl_rep1]


title: leaf_HYPK-knockout_exon2_rep4


title: 9_3G_UcNK_A340_E4_S340 : SS2 sample


title: 11_1i_UcNK_A22_B10_S22 : SS2 sample


title: 4_7H_UtrNK_A11_A11_S11 : SS2 sample


title: 4_7H_UtrNK_A66_F6_S66 : SS2 sample


title: Untransfected_rep4 [Untr_rep4]

value: Untransfected


title: leaf_HYPK-knockout_exon1_rep2


title: 15_4G_UcNK_A320_C8_S320 : SS2 sample


title: Untransfected_rep3 [Untr_rep3]


title: leaf_HYPK-knockout_exon1_rep1


title: 4_7H_UtrNK_A82_G10_S82 : SS2 sample


title: leaf_NAA10-knockdown_rep3

description: Gene expression of Arabidopsis leaves of knockdown of NAA10 via artificial micro RNA


title: leaf_NAA10-knockdown_rep4

value: knockdown of NAA10 via artificial micro RNA


title: 8_1D_UcNK_A275_G11_S275 : SS2 sample


title: leaf_NAA10-knockdown_rep2


title: Untransfected_rep1 [Untr_rep1]


title: te-rep3

city: wenzhou

first: Lijun

last: Chen

state: zhejiang

address: chashan

country: China

institute: wenzhou medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to pig whole genome using hisat2 v2.2.1 with parameters -dta -p 2 -1  -2 -x index -S
FragmentsPer Kilobase per Million (FPKM) were calculated .

organism: Sus scrofa

source_name: in vivo embryo

value: blastomere


title: 11_3E_UtrNK_A228_C12_S228 : SS2 sample

value: mouse maternal-fetal interface


title: 11_1i_UtrNK_A362_G2_S362 : SS2 sample

value: full length (SS2) scRNa-Seq


title: 11_1i_UtrNK_A319_C7_S319 : SS2 sample


title: 4_7H_UcNK_A287_H11_S287 : SS2 sample

value: filtered out of SS2 NK atlas


title: icm_rep2


title: icm_rep1


title: leaf_NAA10-knockdown_rep1


title: 8_1D_UtrNK_A90_H6_S90 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: te-rep2


title: high-affinity ZF with mutation in ZF, replicate 2

city: Boston

first: Ahmad

middle: S

last: Khalil

state: MA

address: 610 Commonwealth Avenue, Rm 405C

department: Biomedical Engineering

country: USA

institute: Boston University

data_processing:
Adapter removal and 3’ quality trimming were performed using cutadapt (Martin, 2011).
Reads were aligned using TopHat2 without a reference transcriptome, against S. cerevisiae genome build R64-2-1 (Engel et al., 2014) modified to include the Venus reporter at the URA3 locus.
Uniquely mapping reads were selected using SAMtools (Li et al., 2009).
Coverage of the 5’-most base of the read (3’-most base of the RNA fragment) was extracted using bedtools genomecov (Quinlan and Hall, 2010), and normalized to the total number of uniquely mapped reads.
RNA-seq differential expression analysis was performed for transcripts of verified coding genes, using an annotation of transcript boundaries based on TIF- (Pelechano et al., 2013) and TSS-seq (Doris et al., 2018) data that was modified to accomodate the Venus reporter at URA3. Read counts over these transcripts were input to differential expression analysis with DESeq2 (Love et al., 2014).
Assembly: S. cerevisiae R-64-2-1
Supplementary files format and content: BigWig file of library-size normalized minus strand coverage of the 5′ end of RNA fragments.
Supplementary files format and content: BigWig file of library-size normalized plus strand coverage of the 5′ end of RNA fragments.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: high-affinity ZF with mutation in ZF

growth_protocol: 50 mL of cells from an overnight culture were induced with β-estradiol and cultured for 7 hours in a 30°C shaking incubator.

extract_protocol:
Cells were brought to the same concentration, spun down for 5 minutes at 1000 RCF at 4°C, liquid was removed and the pellets were resuspended in 600 µL RLT buffer + β-mercaptoethanol. ~600 µL of 0.5 mm diameter glass beads were added and cells were lysed by bead beating on a MagNA Lyser (Roche) three times for 45s each at 4500 RPM with 2 min rests at 4°C. ~300 µL of supernatant was moved into a clean tube, 300 µL of 70% ethanol was added, and samples were processed using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s instructions.
Illumina TruSeq Stranded mRNA

value: high-affinity ZF with mutation in ZF

tag: strain


title: high-affinity ZF with mutation in ZF, replicate 1


title: high-affinity ZF with mutation in ZEV, replicate 2

source_name: high-affinity ZF with mutation in ZEV

value: high-affinity ZF with mutation in ZEV


title: 4_7H_UcNK_A199_A7_S199 : SS2 sample


title: Untransfected_rep2 [Untr_rep2]


title: pLCDM_TSC_rep2

description: pLCDM vs pLCDM_TSC Raw_gene_counts_FPKM_matrix.txt

source_name: Porcine trophoblast stem cell

value: Induced by pLCDM


title: 11_3E_UcNK_A147_E3_S147 : SS2 sample


title: 8_1D_UcNK_A201_A9_S201 : SS2 sample


title: 11_3E_UtrNK_A288_H12_S288 : SS2 sample


title: high-affinity ZF with mutation in ZEV, replicate 1


title: pLCDM_TSC_rep1


title: 9_5B_UtrNK_A253_F1_S253 : SS2 sample


title: reporter-only, replicate 4

source_name: reporter-only

value: reporter-only


title: 15_4G_UtrNK_A159_F3_S159 : SS2 sample


title: 15_4G_UtrNK_A138_D6_S138 : SS2 sample


title: 8_1D_UcNK_A240_D12_S240 : SS2 sample


title: reporter-only, replicate 3


title: 8_1D_UtrNK_A34_C10_S34 : SS2 sample


title: 9_3G_UcNK_A364_G4_S364 : SS2 sample


title: 9_3G_UtrNK_A130_C10_S130 : SS2 sample


title: 4_7H_UtrNK_A16_B4_S16 : SS2 sample


title: pPSC(KOFL)-rep1

description: pLCDM vs pPSC(KOFL) Raw_gene_counts_FPKM_matrix.txt

source_name: Porcine pluripotent stem cell

value: Embryo-derived pluripotent stem cells in pigs


title: pLCDM_rep2

description: pLCDM vs ICM Raw_gene_counts_FPKM_matrix.txt/pLCDM vs TE Raw_gene_counts_FPKM_matrix.txt


title: reporter-only, replicate 2


title: 11_1i_UtrNK_A337_E1_S337 : SS2 sample


title: genomic DNA from stroke patients Discovery 59

type: genomic

city: terrassa

first: NATALIA

last: CULLELL

address: sant antoni 19

country: Spain

institute: fundació mutuaterrassa

description: DNA from whole blood from stroke patients

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 and EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using GenomeStudio using standard recommended Illumina scanner setting

data_processing:
GenomeStudio software
normalized (Noob) Average Beta

label: Cy3 and Cy5

molecule: genomic DNA

source_name: stroke patients first 24 h 28

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the Gentra Puregene Blood Kit (Quiagen, Hilden, Germany)

tag: gender

value: M

tag: delta-nihss


title: pLCDM_rep1


title: 9_3G_UcNK_A300_A12_S300 : SS2 sample


title: 11_3E_UtrNK_A279_H3_S279 : SS2 sample


title: genomic DNA from stroke patients Discovery 58

source_name: stroke patients first 24 h 16


title: 11_3E_UtrNK_A237_D9_S237 : SS2 sample


title: 9_5B_UtrNK_A217_C1_S217 : SS2 sample


title: 15_4G_UtrNK_A190_H10_S190 : SS2 sample


title: high-affinity ZF, replicate 4

source_name: high-affinity ZF

value: high-affinity ZF


title: 11_1i_UtrNK_A328_D4_S328 : SS2 sample


title: reporter-only, replicate 1


title: high-affinity ZF, replicate 1


title: genomic DNA from stroke patients Discovery 57

source_name: stroke patients first 24 h 33


title: pPSC(KOFL)-rep2


title: 8_1D_UcNK_A211_B7_S211 : SS2 sample

source_name: mouse maternal-fetal interface


title: 11_1i_UcNK_A87_H3_S87 : SS2 sample


title: 9_3G_UcNK_A343_E7_S343 : SS2 sample


title: low-affinity ZF, replicate 4

source_name: low-affinity ZF

value: low-affinity ZF


title: 15_4G_UtrNK_A181_H1_S181 : SS2 sample


title: low-affinity ZF, replicate 3


title: genomic DNA from stroke patients Discovery 55

source_name: stroke patients first 24 h 14


title: 9_3G_UcNK_A301_B1_S301 : SS2 sample


title: 4_7H_UtrNK_A28_C4_S28 : SS2 sample


title: low-affinity ZF, replicate 2


title: 9_3G_UcNK_A314_C2_S314 : SS2 sample


title: 8_1D_UcNK_A272_G8_S272 : SS2 sample


title: genomic DNA from stroke patients Discovery 54

source_name: stroke patients first 24 h 24

value: F


title: high-affinity ZF, replicate 2


title: 15_4G_UcNK_A371_G11_S371 : SS2 sample


title: 11_1i_UcNK_A7_A7_S7 : SS2 sample


title: low-affinity ZF, replicate 1


title: 11_1i_UtrNK_A308_B8_S308 : SS2 sample


title: genomic DNA from stroke patients Discovery 53

source_name: stroke patients first 24 h 4


title: 8_1D_UcNK_A251_E11_S251 : SS2 sample


title: 11_3E_UtrNK_A240_D12_S240 : SS2 sample


title: low-affinity ZF with clamp, replicate 4

source_name: low-affinity ZF with clamp

value: low-affinity ZF with clamp


title: genomic DNA from stroke patients Discovery 52

source_name: stroke patients first 24 h 5


title: genomic DNA from stroke patients Discovery 51

source_name: stroke patients first 24 h 29


title: genomic DNA from stroke patients Discovery 56

source_name: stroke patients first 24 h 32


title: low-affinity ZF with clamp, replicate 3


title: low-affinity ZF with clamp, replicate 1


title: 11_1i_UcNK_A77_G5_S77 : SS2 sample


title: 11_3E_UtrNK_A216_B12_S216 : SS2 sample


title: low-affinity ZF with clamp, replicate 2


title: 8_1D_UtrNK_A48_D12_S48 : SS2 sample


title: 9_5B_UtrNK_A270_G6_S270 : SS2 sample


title: genomic DNA from stroke patients Discovery 50

source_name: stroke patients first 24 h 10


title: 11_3E_UtrNK_A205_B1_S205 : SS2 sample


title: healthy MNs (ctr_r4)

city: Exeter

first: Akshay

last: Bhinge

address: Stocker Road

department: CBS

institute: Living Systems Institute, University of Exeter

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt
Trimmed sequence reads were mapped to hg19 using bowtie. Forward reads from the paired-end files were combined with single reads for generating bam files using bowtie.
Read counts were estimated using R package feature count and normalization were performed using DESeq2
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw readcounts per gene for each Sample

source_name: iPSC

extract_protocol:
RNA was harvested using microRNeasy mini kit (Qiagen).
1.0 ug of total RNA was used to construct sequencing libraries using the Lexogen 3'end FWD kit.

value: iPSC

value: iPSC-derived motor neuron

value: healthy

value: motor neuron differentiation

tag: time

value: Day 34

value: control


title: healthy MNs (ctr_r3)


title: 15_4G_UtrNK_A140_D8_S140 : SS2 sample

tag: tissue

value: mouse maternal-fetal interface

value: full length (SS2) scRNa-Seq

value: maternal-fetal NK interface atlas (SS2)


title: genomic DNA from stroke patients Discovery 48

source_name: stroke patients first 24 h 26


title: genomic DNA from stroke patients Discovery 47

source_name: stroke patients first 24 h 3


title: genomic DNA from stroke patients Discovery 46

source_name: stroke patients first 24 h 22


title: 15_4G_UtrNK_A129_C9_S129 : SS2 sample

tag: genotype


title: 9_3G_UtrNK_A112_B4_S112 : SS2 sample

tag: sample id

value: filtered out of SS2 NK atlas


title: 8_1D_UtrNK_A83_G11_S83 : SS2 sample

tag: mouse id


title: 8_1D_UtrNK_A81_G9_S81 : SS2 sample

tag: technology


title: 11_1i_UtrNK_A351_F3_S351 : SS2 sample

tag: atlas


title: healthy MNs (ctr_r2)


title: healthy MNs (mir_r4)

value: miR-139 overexpression


title: 11_3E_UcNK_A107_A11_S107 : SS2 sample


title: 15_4G_UcNK_A303_B3_S303 : SS2 sample


title: genomic DNA from stroke patients Discovery 45

source_name: stroke patients first 24 h 30


title: genomic DNA from stroke patients Discovery 49

source_name: stroke patients first 24 h 17


title: 9_5B_UtrNK_A227_C11_S227 : SS2 sample


title: genomic DNA from stroke patients Discovery 44

source_name: stroke patients first 24 h 6


title: genomic DNA from stroke patients Discovery 42

source_name: stroke patients first 24 h 15


title: 15_4G_UtrNK_A123_C3_S123 : SS2 sample

source_name: mouse maternal-fetal interface


title: genomic DNA from stroke patients Discovery 43

source_name: stroke patients first 24 h 23


title: 9_3G_UtrNK_A116_B8_S116 : SS2 sample


title: genomic DNA from stroke patients Discovery 39

source_name: stroke patients first 24 h 12


title: FUS H517Q heterozygous (FUS_het_2)

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using the FastX-toolkit
Trimmed sequence reads were mapped to hg19 using bowtie
Read counts were estimated using R package feature count and normalization were performed using DESeq2
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw readcounts per microRNA for each Sample

extract_protocol:
RNA was harvested using microRNeasy mini kit (Qiagen).
1.0 ug of total RNA was used to construct sequencing libraries using the NEBNext Small RNA kit

value: ALS

value: Day 30


title: 4_7H_UcNK_A195_A3_S195 : SS2 sample


title: 4_7H_UcNK_A281_H5_S281 : SS2 sample


title: healthy MNs (mir_r2)


title: 11_3E_UcNK_A182_H2_S182 : SS2 sample


title: FUS H517Q heterozygous (FUS_het_1)


title: healthy MNs (79A_2)


title: healthy MNs (79A_1)


title: 11_1i_UcNK_A55_E7_S55 : SS2 sample


title: 15_4G_UcNK_A378_H6_S378 : SS2 sample


title: genomic DNA from stroke patients Discovery 41

source_name: stroke patients first 24 h 25

value: M


title: 11_3E_UtrNK_A274_G10_S274 : SS2 sample


title: 8_1D_UtrNK_A51_E3_S51 : SS2 sample


title: genomic DNA from stroke patients Discovery 37

source_name: stroke patients first 24 h 8


title: healthy MNs (80A_2)


title: 9_5B_UtrNK_A243_E3_S243 : SS2 sample


title: 11_1i_UcNK_A96_H12_S96 : SS2 sample


title: 9_3G_UcNK_A306_B6_S306 : SS2 sample


title: genomic DNA from stroke patients Discovery 40

source_name: stroke patients first 24 h 34


title: 4_7H_UtrNK_A94_H10_S94 : SS2 sample


title: 8_1D_UcNK_A230_D2_S230 : SS2 sample


title: healthy MNs (mir_r3)


title: 11_3E_UtrNK_A211_B7_S211 : SS2 sample


title: FUS H517Q homozygous (FUS_hom_2)


title: FUS H517Q homozygous (FUS_hom_1)


title: healthy MNs (80A_1)


title: genomic DNA from stroke patients Discovery 38

source_name: stroke patients first 24 h 7


title: 11_1i_UcNK_A31_C7_S31 : SS2 sample


title: genomic DNA from stroke patients Discovery 34

source_name: stroke patients first 24 h 20


title: MC2 155_crp2 mutant_rep3

city: Pusan

first: Eon-Min

last: Ko

address: pusandaehak-ro

country: South Korea

institute: Pusan national university

data_processing:
The quality of the obtained data was checked by determining the phred quality score using FastQC v0.11.5.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.32, then mapped to the whole genome of M. smegmatis using bowtie v1.1.2 with default setting.
Mapped reads per annotated gene were counted by Bam2readcount.
Counted values were nomalized in the RPKM method.
Assembly: Mycobacterium smegmatis MC2 155 (GCF_000015005.1_ASM1500v1)
Supplementary files format and content: txt: tab-delimited text files include RPKM values for each sample

organism: Mycolicibacterium smegmatis

growth_protocol: The M. smegmatis strains were grown aerobically in Middlebrook 7H9 medium supplemented with 0.2% glucose and 0.02% Tween 80 (vol/vol) on a gyratory shaker (200 rpm) at 37°C.

extract_protocol:
The stains were grown until an optical density at 600 nm reached 2.0 to 2.1. Cells were harvested by centrifugation at 4°C with 3500×g for 3 min. The cell pellets were resuspended with 1 ml TRIzol (Invitrogen). Procedures of total RNA extract from the cell pellets were performed using TRIZol purchased from Invitrogen and followed the instructions provided to users. Six ibraries for RNA-seq were prepared using the Illumina TruSeqTM RNA sample prep kit with the standard low-throughput protocol. Sequencing was performed on an Illumina HiSeq2000 instrument.
The RNA sequencing libraries were created using a TruSeq RNA Sample Prep Kit v2 (Illumina) with the standard low-throughput protocol.

tag: genotype/variation

tag: conditions

value: in vitro


title: 9_3G_UtrNK_A172_G4_S172 : SS2 sample


title: 8_1D_UtrNK_A43_D7_S43 : SS2 sample


title: genomic DNA from stroke patients Discovery 35

source_name: stroke patients first 24 h 31


title: 15_4G_UcNK_A298_A10_S298 : SS2 sample


title: MC2 155_crp2 mutant_rep1


title: 11_3E_UtrNK_A206_B2_S206 : SS2 sample


title: genomic DNA from stroke patients Discovery 36

source_name: stroke patients first 24 h 1


title: 11_1i_UtrNK_A326_D2_S326 : SS2 sample


title: 9_5B_UtrNK_A241_E1_S241 : SS2 sample


title: MC2 155_crp2 mutant_rep2


title: 9_5B_UcNK_A76_G4_S76 : SS2 sample


title: 15_4G_UcNK_A304_B4_S304 : SS2 sample


title: genomic DNA from stroke patients Discovery 33

source_name: stroke patients first 24 h 2

value: F


title: genomic DNA from stroke patients Discovery 31

source_name: stroke patients first 24 h 13


title: 4_7H_UtrNK_A54_E6_S54 : SS2 sample


title: 4_7H_UtrNK_A41_D5_S41 : SS2 sample


title: MC2 155_WT_rep1

value: wild type


title: 15_4G_UcNK_A333_D9_S333 : SS2 sample


title: 11_3E_UcNK_A177_G9_S177 : SS2 sample


title: genomic DNA from stroke patients Discovery 30

source_name: stroke patients first 24 h 11


title: MC2 155_WT_rep2


title: 11_1i_UcNK_A65_F5_S65 : SS2 sample


title: 9_3G_UcNK_A374_H2_S374 : SS2 sample


title: genomic DNA from stroke patients Discovery 32

source_name: stroke patients first 24 h 18


title: 9_5B_UcNK_A77_G5_S77 : SS2 sample


title: 9_5B_UcNK_A21_B9_S21 : SS2 sample


title: genomic DNA from stroke patients Discovery 29

source_name: stroke patients first 24 h 9


title: 9_3G_UtrNK_A189_H9_S189 : SS2 sample


title: Time15_sample20

city: Jouy-en-Josas

first: Cyprien

last: Guérin

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE

data_processing:
Read mapping using BWA-backtrack (version 0.7.12-r1039).
Structural reference annotation of Enterococcus faecalis V583 chromosome (AE016830.1) was enriched with sRNA annotation from Innocenti et al., 2015.
Read counts were obtained using HTSeq-count (version 0.9.1).
Differential expression analysis R library "DESeq2" and associated "median ratio method" normalization procedure.
DESeq2 p-values were converted into q-values using R library "fdrtool".
RPKM values processed using DESeq-2 with a prior-count of 33.
Genome_build: Enterococcus faecalis V583 chromosome (AE016830.1)
Supplementary_files_format_and_content: TCA_gene_expression.txt: Tab-delimited text file containing for each gene/sample raw data counts, log2rpkm with differential expression analysis results.

organism: Enterococcus faecalis

source_name: Cell culture

growth_protocol: E. faecalis strains were grown in standardized conditions as described in Fouquier D'hérouel, 2011. For all experiments, the strain frozen at -80°C was streaked on 1.5 % agar plate of Brain Heart Infusion (BHI), grown for 20 h at 37°C and incubated 2 h at room temperature. One single colony was used to inoculate 5 ml of liquid BHI and grown for 18 h at 37°C without agitation. The culture was then diluted 1/500-fold in a pre-warmed BHI liquid medium and grown to an OD600 ranging from 0.27 to 0.33 (OD600 ~ 0.3), as monitored manually on spectrophotometer at 600 nm weight length (Pharmacia Biotech, Novaspec II). At such a density, the bacterial population ranged from ~2 to 4 x 10^8 cfu/mL, as verified by viable cell counts on BHI plates.

extract_protocol:
Fouquier D'hérouel et al., 2011.
Innocenti et al., 2015 and Lacoux et al., 2020.

treatment_protocol: Fouquier D'hérouel et al., 2011; Lacoux et al., 2020.

tag: treatment

value: TCA

tag: time point (minutes)

tag: biological replicate


title: 8_1D_UcNK_A241_E1_S241 : SS2 sample


title: genomic DNA from stroke patients Discovery 28

source_name: stroke patients first 24 h 27


title: MC2 155_WT_rep3


title: genomic DNA from stroke patients Discovery 27

source_name: stroke patients first 24 h 19


title: 9_3G_UcNK_A349_F1_S349 : SS2 sample

source_name: mouse maternal-fetal interface


title: 4_7H_UcNK_A196_A4_S196 : SS2 sample


title: 11_1i_UcNK_A64_F4_S64 : SS2 sample


title: 9_3G_UtrNK_A175_G7_S175 : SS2 sample


title: genomic DNA from stroke patients Discovery 26

source_name: stroke patients first 24 h 21


title: 11_3E_UtrNK_A254_F2_S254 : SS2 sample


title: Time06_sample18


title: Time03_sample17


title: 4_7H_UtrNK_A83_G11_S83 : SS2 sample


title: Time00_sample16


title: 9_5B_UcNK_A57_E9_S57 : SS2 sample


title: genomic DNA from stroke patients Discovery 24

source_name: stroke patients first 24 h 48


title: 11_1i_UcNK_A30_C6_S30 : SS2 sample


title: genomic DNA from stroke patients Discovery 23

source_name: stroke patients first 24 h 46


title: 9_5B_UtrNK_A201_A9_S201 : SS2 sample


title: Time15_sample15


title: genomic DNA from stroke patients Discovery 22

source_name: stroke patients first 24 h 54


title: Time10_sample14


title: 4_7H_UcNK_A261_F9_S261 : SS2 sample


title: 15_4G_UtrNK_A185_H5_S185 : SS2 sample


title: Time10_sample19


title: 4_7H_UcNK_A214_B10_S214 : SS2 sample


title: Time06_sample13


title: genomic DNA from stroke patients Discovery 21

source_name: stroke patients first 24 h 56


title: Time03_sample12


title: 11_3E_UcNK_A121_C1_S121 : SS2 sample


title: 8_1D_UtrNK_A87_H3_S87 : SS2 sample


title: genomic DNA from stroke patients Discovery 25

source_name: stroke patients first 24 h 49


title: genomic DNA from stroke patients Discovery 20

source_name: stroke patients first 24 h 40


title: 15_4G_UtrNK_A122_C2_S122 : SS2 sample


title: genomic DNA from stroke patients Discovery 19

source_name: stroke patients first 24 h 37


title: Time00_sample11


title: 11_3E_UcNK_A117_B9_S117 : SS2 sample


title: Time15_sample10


title: 11_1i_UtrNK_A336_D12_S336 : SS2 sample


title: 8_1D_UcNK_A232_D4_S232 : SS2 sample


title: 4_7H_UtrNK_A91_H7_S91 : SS2 sample


title: 11_3E_UcNK_A170_G2_S170 : SS2 sample


title: genomic DNA from stroke patients Discovery 18

source_name: stroke patients first 24 h 35


title: Time06_sample8


title: 9_3G_UtrNK_A131_C11_S131 : SS2 sample


title: 9_5B_UcNK_A29_C5_S29 : SS2 sample


title: Time10_sample9


title: genomic DNA from stroke patients Discovery 16

source_name: stroke patients first 24 h 38


title: genomic DNA from stroke patients Discovery 15

source_name: stroke patients first 24 h 42


title: genomic DNA from stroke patients Discovery 17

source_name: stroke patients first 24 h 36


title: 8_1D_UcNK_A213_B9_S213 : SS2 sample


title: 9_5B_UtrNK_A232_D4_S232 : SS2 sample


title: 8_1D_UtrNK_A76_G4_S76 : SS2 sample


title: Time00_sample6


title: 9_5B_UtrNK_A271_G7_S271 : SS2 sample


title: 9_3G_UcNK_A321_C9_S321 : SS2 sample


title: genomic DNA from stroke patients Discovery 14

source_name: stroke patients first 24 h 41


title: Time15_sample5

source_name: Cell culture


title: genomic DNA from stroke patients Discovery 12

source_name: stroke patients first 24 h 58


title: genomic DNA from stroke patients Discovery 13

source_name: stroke patients first 24 h 39


title: 4_7H_UtrNK_A55_E7_S55 : SS2 sample

source_name: mouse maternal-fetal interface


title: 9_5B_UtrNK_A276_G12_S276 : SS2 sample


title: Time06_sample3


title: Time10_sample4


title: 11_1i_UcNK_A56_E8_S56 : SS2 sample


title: 8_1D_UcNK_A236_D8_S236 : SS2 sample


title: 11_1i_UcNK_A40_D4_S40 : SS2 sample


title: 9_5B_UcNK_A31_C7_S31 : SS2 sample


title: Time03_sample7


title: 8_1D_UcNK_A214_B10_S214 : SS2 sample


title: Time03_sample2


title: 9_3G_UtrNK_A174_G6_S174 : SS2 sample


title: genomic DNA from stroke patients Discovery 9

source_name: stroke patients first 24 h 57


title: genomic DNA from stroke patients Discovery 11

source_name: stroke patients first 24 h 59


title: Time00_sample1


title: 8_1D_UcNK_A219_C3_S219 : SS2 sample


title: genomic DNA from stroke patients Discovery 8

source_name: stroke patients first 24 h 53


title: 8_1D_UcNK_A260_F8_S260 : SS2 sample


title: genomic DNA from stroke patients Discovery 7

source_name: stroke patients first 24 h 44


title: 9_3G_UtrNK_A119_B11_S119 : SS2 sample


title: 11_3E_UtrNK_A272_G8_S272 : SS2 sample


title: 11_3E_UtrNK_A213_B9_S213 : SS2 sample


title: genomic DNA from stroke patients Discovery 5

source_name: stroke patients first 24 h 51


title: 8_1D_UtrNK_A37_D1_S37 : SS2 sample


title: 9_5B_UtrNK_A219_C3_S219 : SS2 sample


title: 11_1i_UcNK_A46_D10_S46 : SS2 sample


title: genomic DNA from stroke patients Discovery 6

source_name: stroke patients first 24 h 45


title: 15_4G_UtrNK_A107_A11_S107 : SS2 sample


title: genomic DNA from stroke patients Discovery 4

source_name: stroke patients first 24 h 50


title: 11_3E_UtrNK_A219_C3_S219 : SS2 sample


title: microglial cells, APP, Aged, female (SAMPLE 36)

city: Dublin

first: Virginia

last: Mela

address: Trinity College Dublin

country: Ireland

institute: Trinity College Institute of Neuroscience

description: SAMPLE 36

hyb_protocol: According to the manufacturer’s instructions

scan_protocol: nCounter analysis system

data_processing:
nCounter MAX Analysis system
Data analysis was performed using nSolver software; negative and positive controls were used to normalize for variability in hybridization, purification or binding. Raw data were normalized using the geometric mean of housekeeping genes

source_name: microglial cells

growth_protocol: cells were plate in 12 well plate (500000 cells/plate) and maintained 5 days in vitro

extract_protocol: RNA was isolated from microglia (400,000 cells/well in 12-well plates; final volume 800ml) using the NucleoSpin RNA II kit (Macherey-Nagel, Duren, Germany) and stored at -80°C

tag: cell type

value: microglial cells

value: 5 days in vitro

value: APP

value: Aged

tag: Sex

value: female


title: 11_1i_UcNK_A79_G7_S79 : SS2 sample

value: mouse maternal-fetal interface


title: genomic DNA from stroke patients Discovery 10

source_name: stroke patients first 24 h 52

tag: age


title: microglial cells, Wild  type, Aged, male (SAMPLE 33)

description: SAMPLE 33

value: Wild  type

value: male


title: microglial cells, Wild  type, Aged, female (SAMPLE 35)

description: SAMPLE 35


title: 11_1i_UtrNK_A384_H12_S384 : SS2 sample

value: full length (SS2) scRNa-Seq

value: filtered out of SS2 NK atlas


title: genomic DNA from stroke patients Discovery 3

source_name: stroke patients first 24 h 55

tag: gender


title: 4_7H_UcNK_A272_G8_S272 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: 9_5B_UcNK_A20_B8_S20 : SS2 sample


title: 8_1D_UcNK_A195_A3_S195 : SS2 sample


title: microglial cells, APP, Young, female (SAMPLE 32)

description: SAMPLE 32

value: Young


title: 15_4G_UtrNK_A135_D3_S135 : SS2 sample


title: genomic DNA from stroke patients Discovery 2

source_name: stroke patients first 24 h 47

tag: delta-nihss


title: genomic DNA from stroke patients Discovery 1

source_name: stroke patients first 24 h 43


title: microglial cells, Wild  type, Young, male (SAMPLE 31)

description: SAMPLE 31

tag: time


title: 9_5B_UcNK_A35_C11_S35 : SS2 sample

tag: tissue


title: 8_1D_UtrNK_A63_F3_S63 : SS2 sample

tag: genotype


title: microglial cells, APP, Aged, male (SAMPLE 34)

description: SAMPLE 34


title: 4_7H_UcNK_A204_A12_S204 : SS2 sample

tag: sample id


title: microglial cells, Wild  type, Aged, female (SAMPLE 29)

description: SAMPLE 29


title: microglial cells, APP, Aged, male (SAMPLE 28)

description: SAMPLE 28


title: 204_G9_MLT

city: BARCELONA

first: Alejandro

last: Valdivieso

state: BARCELONA

address: PASSEIG MARÍTIM DE LA BARCELONETA, 37-49

institute: Insituto de Ciencias del Mar

library_source: genomic

data_processing:
raw reads were quality trimmed by the Trim Galore! software (v. 0.4.5) with the following parameters  --nextera, --quality 20, and --phred64
adapters, the number and quality of the reads were checked using the FastQC software (v. 0.11.6)
the alignments of the pair-end reads were performed using the function “bismark”: --bowtie2, --non-directional, and --score_min 0 + (−0.6 x read length). Bismark software (v. 16.0)
methylation calling  bismark_methylation_extractor”: --bedGraph
Genome_build: GRCz10 Danio rerio https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.5/
Supplementary_files_format_and_content: tab-delimited files (sample_name.txt) contain the coverage and the frequency of Cs (methylated cytosines) and of Ts (unmethylated cytosines) per CpG (chromosome, base, strand) covered

organism: Danio rerio

source_name: Testis

growth_protocol: Zebrafish were raised following:  Westerfield, M. (2000). The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio). 4th ed., Univ. of Oregon Press, Eugene.

extract_protocol:
Phenol-Chlorofrom DNA extraction
library preparation following protocol as in Anastasiadi et al 2018
Gonads were extracted, flash frozen in nitrogen liquid. DNA was extracted  following  the Phenol-Chlorofrom DNA extraction. Bisulfite conversion was carried out using D5020, Zymo Research from 1000 ng of genomic DNA in each sample. Illumina Hiseq 2500 was used for sequencing the library.
Library was constructed following the Illumina’s protocol: “16S metagenomic library preparation” using Nextera XT Index Kit V2 set A, FC-131–2001 kit.

treatment_protocol: Thermal treatment was exactly as described in Ribas, Laia, et al. "Heat-induced masculinization in domesticated zebrafish is family-specific and yields a set of different gonadal transcriptomes." Proceedings of the National Academy of Sciences 114.6 (2017): E941-E950.

tag: strain

value: AB

tag: FISH origin

value: laboratory (reared in aquarium facilities)

value: 90 days old

value: Testis

value: LT


title: 9_3G_UcNK_A322_C10_S322 : SS2 sample

tag: mouse id

tag: technology

tag: atlas


title: 4_7H_UcNK_A262_F10_S262 : SS2 sample


title: 8_1D_UcNK_A209_B5_S209 : SS2 sample


title: 11_1i_UcNK_A4_A4_S4 : SS2 sample


title: microglial cells, Wild  type, Aged, male (SAMPLE 27)

description: SAMPLE 27

value: microglial cells


title: microglial cells, APP, Young, female (SAMPLE 26)

description: SAMPLE 26

value: 5 days in vitro


title: 15_4G_UtrNK_A187_H7_S187 : SS2 sample


title: 204_G8_MLT

tag: treatment


title: 8_1D_UtrNK_A82_G10_S82 : SS2 sample


title: 204_G7_MLT


title: 204_G8_MHT

value: HT


title: 11_3E_UtrNK_A248_E8_S248 : SS2 sample


title: microglial cells, APP, Aged, female (SAMPLE 24)

description: SAMPLE 24

value: APP

value: Aged


title: 4_7H_UtrNK_A57_E9_S57 : SS2 sample

value: mouse maternal-fetal interface


title: 4_7H_UtrNK_A92_H8_S92 : SS2 sample


title: 11_3E_UcNK_A114_B6_S114 : SS2 sample


title: 204_G7_FHT

source_name: Ovaries

value: Ovaries


title: mouse EPN, Sox9-GOF, ChIP-H3K27ac, rep2

city: Houston

first: Debosmita

last: Sardar

address: 1 Baylor Plaza

institute: Baylor College of Medicine

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: mouse EPN tumor tissue

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.

value: mouse EPN tumor tissue

value: EPN Sox9-GOF


title: 4_7H_UtrNK_A36_C12_S36 : SS2 sample

value: full length (SS2) scRNa-Seq


title: microglial cells, Wild  type, Aged, female (SAMPLE 23)

description: SAMPLE 23

value: Wild  type

value: female


title: microglial cells, Wild  type, Young, male (SAMPLE 25)

description: SAMPLE 25

value: Young

value: male


title: 204_G6_FHT

value: AB

value: laboratory (reared in aquarium facilities)

value: 90 days old


title: 4_7H_UcNK_A286_H10_S286 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: 204_G6_FLT

value: LT


title: 4_7H_UcNK_A283_H7_S283 : SS2 sample

value: filtered out of SS2 NK atlas


title: mouse EPN, Sox9-GOF, Input, rep2


title: 15_4G_UcNK_A354_F6_S354 : SS2 sample


title: mouse EPN, Sox9-GOF, ChIP-H3K27ac, rep1


title: 204_G9_FHT

value: HT


title: microglial cells, APP, Aged, male (SAMPLE 22)

description: SAMPLE 22

value: microglial cells

value: 5 days in vitro

value: APP

value: Aged


title: microglial cells, Wild  type, Aged, male (SAMPLE 21)

description: SAMPLE 21


title: 204_G5_MLT

value: Testis


title: microglial cells, APP, Young, female (SAMPLE 20)

description: SAMPLE 20


title: mouse HGG, Sox9-GOF, ChIP-H3K27ac, rep2

source_name: mouse HGG tumor tissue

value: mouse HGG tumor tissue

value: HGG Sox9-GOF


title: 4_7H_UcNK_A280_H4_S280 : SS2 sample

source_name: mouse maternal-fetal interface

value: mouse maternal-fetal interface

value: full length (SS2) scRNa-Seq


title: 204_G5_FHT

value: Ovaries


title: mouse HGG, Sox9-GOF, Input, rep2


title: 15_4G_UcNK_A294_A6_S294 : SS2 sample


title: 8_1D_UcNK_A222_C6_S222 : SS2 sample


title: microglial cells, Wild  type, Young, female (SAMPLE 19)

description: SAMPLE 19

value: Wild  type

value: Young

value: female


title: 15_4G_UtrNK_A162_F6_S162 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: 204_G4_FLT

value: AB

value: laboratory (reared in aquarium facilities)

value: 90 days old

value: LT


title: microglial cells, APP, Aged, female (SAMPLE 18)

description: SAMPLE 18

value: microglial cells

value: 5 days in vitro


title: 204_G3_MLT


title: mouse EPN, Sox9-GOF, Input, rep1

value: mouse EPN tumor tissue

value: EPN Sox9-GOF


title: 11_1i_UtrNK_A344_E8_S344 : SS2 sample

value: filtered out of SS2 NK atlas


title: 204_G4_FHT

value: HT


title: 204_G3_FHT


title: 204_G20_FLT


title: mouse HGG, Sox9-LOF, ChIP-H3K27ac, rep2

value: mouse HGG tumor tissue

value: HGG Sox9-LOF


title: microglial cells, Wild  type, Aged, male (SAMPLE 15)

description: SAMPLE 15

value: Aged

value: male


title: 15_4G_UtrNK_A128_C8_S128 : SS2 sample

value: mouse maternal-fetal interface

value: full length (SS2) scRNa-Seq


title: microglial cells, APP, Young, male (SAMPLE 14)

description: SAMPLE 14

value: APP

value: Young


title: mouse HGG, Sox9-LOF, Input, rep2


title: 11_1i_UcNK_A24_B12_S24 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: microglial cells, Wild  type, Young, female (SAMPLE 13)

description: SAMPLE 13

value: Wild  type

value: female


title: 204_G20_FHT

value: AB

value: laboratory (reared in aquarium facilities)

value: 90 days old

value: Ovaries


title: microglial cells, Wild  type, Aged, female (SAMPLE 17)

description: SAMPLE 17

value: microglial cells

value: 5 days in vitro


title: mouse HGG, Sox9-GOF, ChIP-H3K27ac, rep1

value: mouse HGG tumor tissue

value: HGG Sox9-GOF


title: 9_3G_UtrNK_A102_A6_S102 : SS2 sample


title: microglial cells, APP, Aged, male (SAMPLE 16)

description: SAMPLE 16

value: Aged


title: 204_G2_MHT

value: Testis

value: HT


title: mouse HGG, Sox9-LOF, Input, rep1

value: HGG Sox9-LOF


title: mouse HGG, Sox9-GOF, Input, rep1


title: 204_G2_MLT

value: LT


title: mouse EPN, control, ChIP-H3K27ac, rep2

value: mouse EPN tumor tissue

value: control

value: EPN control


title: microglial cells, Wild  type, Aged, female (SAMPLE 11)

description: SAMPLE 11

value: Wild  type

value: female


title: microglial cells, APP, Aged, female (SAMPLE 12)

description: SAMPLE 12

value: APP


title: 11_3E_UcNK_A125_C5_S125 : SS2 sample

value: mouse maternal-fetal interface

value: full length (SS2) scRNa-Seq

value: maternal-fetal NK interface atlas (SS2)


title: 204_G19_MHT

value: AB

value: laboratory (reared in aquarium facilities)

value: 90 days old


title: mouse EPN, control, Input, rep2


title: 9_5B_UcNK_A78_G6_S78 : SS2 sample


title: 204_G19_FLT

value: Ovaries


title: 11_3E_UtrNK_A271_G7_S271 : SS2 sample


title: microglial cells, APP, Aged, male (SAMPLE 10)

description: SAMPLE 10

value: microglial cells

value: 5 days in vitro

value: Aged

value: male


title: microglial cells, Wild  type, Aged, male (SAMPLE 9)

description: SAMPLE 9


title: microglial cells, APP, Young, female (SAMPLE 8)

description: SAMPLE 8

value: Young


title: 4_7H_UcNK_A223_C7_S223 : SS2 sample


title: 204_G17_MLT

value: Testis

value: LT


title: mouse HGG, Sox9-LOF, ChIP-H3K27ac, rep1

value: mouse HGG tumor tissue

value: HGG Sox9-LOF


title: 204_G18_MHT

value: HT


title: mouse HGG, control, ChIP-H3K27ac, rep2

value: control

value: HGG control


title: microglial cells, Wild  type, Young, female (SAMPLE 7)

description: SAMPLE 7

value: Wild  type

value: female


title: mouse EPN, control, Input, rep1

value: mouse EPN tumor tissue

value: EPN control


title: 11_3E_UcNK_A191_H11_S191 : SS2 sample

value: mouse maternal-fetal interface

value: full length (SS2) scRNa-Seq

value: filtered out of SS2 NK atlas


title: 9_5B_UtrNK_A261_F9_S261 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: 204_G16_FLT

value: AB

value: laboratory (reared in aquarium facilities)

value: 90 days old

value: Ovaries


title: 9_5B_UcNK_A50_E2_S50 : SS2 sample


title: 204_G17_MHT

value: Testis


title: mouse EPN, control, ChIP-H3K27ac, rep1


title: 8_1D_UcNK_A221_C5_S221 : SS2 sample


title: microglial cells, APP, Aged, female (SAMPLE 6)

description: SAMPLE 6

value: microglial cells

value: 5 days in vitro

value: APP

value: Aged


title: 204_G16_FHT

value: HT


title: 9_3G_UtrNK_A117_B9_S117 : SS2 sample


title: mouse HGG, control, Input, rep1

value: mouse HGG tumor tissue

value: control

value: HGG control


title: 15_4G_UcNK_A353_F5_S353 : SS2 sample

value: mouse maternal-fetal interface


title: mouse HGG, control, Input, rep2


title: mouse HGG, control, ChIP-H3K27ac, rep1


title: 11_3E_UtrNK_A239_D11_S239 : SS2 sample

value: full length (SS2) scRNa-Seq


title: microglial cells, Wild  type, Aged, female (SAMPLE 5)

description: SAMPLE 5

value: Wild  type

value: female


title: 204_G14_MLT

value: AB

value: LT


title: mouse tissue, EPN Sox9-GOF, rep 2

data_processing:
Quality control was performed using fastQC (v0.11.7) and MultiQC (v1.11).
Reads were mapped to the mouse genome mm10 assembly using STAR (v2.5.0a). Mapped reads were used to build count matrices using Bioconductor packages GenomicAlignments (v1.26.0) and GenomicFeatures (v1.42.2).
UCSC transcripts were downloaded from Illumina iGenomes in GTF file format.
DESeq2 (v1.30.1) was used for normalization and differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPM values

source_name: brain tumor tissue

extract_protocol:
Tumor tissue was collected and frozen in trizol. After thaw, tissues were dissociated and total RNA was isolated using trizol and chloroform, and purified using the RNeasy Mini Kit (QIAGEN).
Illumina sequencing libraries with 6-bp single indices were constructed from 300 ng total RNA using the TruSeq Stranded mRNA LT kit (Illumina, RS-122-2101).

value: brain tumor tissue

value: EPN Sox9-GOF


title: 9_5B_UcNK_A16_B4_S16 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: microglial cells, APP, Aged, male (SAMPLE 4)

description: SAMPLE 4

value: microglial cells

value: male


title: 204_G15_MLT

value: laboratory (reared in aquarium facilities)

value: 90 days old

value: Testis


title: fLow3

city: Tempe

first: César

middle: Ivan

last: Torres

state: AZ

address: 797 E. Tyler St.

institute: Arizona State University

data_processing:
Basecalling with CASAVA
Trimming paired end reads with trimmomatic
Aligning to reference sequence with Bowtie2, keeping union alignments only
Convert from .SAM to .BAM with Samtools
Use R packages GenomicAlignments and DeSEQ2 to assign counts to genes and normalize for statistical analysis
Assembly: GCF_000007985.2_ASM798v2
Supplementary files format and content: FPKM data in Excel workbook was created with the fpkm(robust=TRUE) function Deseq2 in R with replicates collapsed into a single value. FPKM was not used for statistical analysis in the associated publications
Supplementary files format and content: .csv file of counts per gene was made with the GenomicRanges package in R. This is the data used in DESeq2 analysis downstream

organism: Geobacter sulfurreducens PCA

source_name: Geobacter sulfurreducens PCA

growth_protocol: Planktonic cells were grown in anaerobic tubes for 7 days. Biofilm cells were grown in anaerobic bioreactors on graphite electrodes poised at the listed potentials.

extract_protocol:
Qiagen PowerMicrobiome kit. Biofilm samples were scraped and then immediately extracted. Planktonic samples were spun down and then the pellet went into the extraction.
rRNA was partially depleted with the Thermofisher bacterial mRNA enrichment kit, then the KAPA Biosystems Hyperprep RNA kit with barcoding was used to prepare libraries. Samples 1-12 and samples 13-21 were sequenced on separate runs to a comparable read depth.

tag: electron donor

value: Formate

tag: electron acceptor

value: anode

tag: anode potential [v vs. she]

value: biofilm


title: 204_G15_FHT

value: Ovaries

value: HT


title: 15_4G_UtrNK_A119_B11_S119 : SS2 sample

value: mouse maternal-fetal interface

value: full length (SS2) scRNa-Seq


title: microglial cells, Wild  type, Aged, male (SAMPLE 3)

description: SAMPLE 3

tag: cell type

value: 5 days in vitro

value: Wild  type

value: Aged

tag: Sex


title: microglial cells, Wild  type, Young, male (SAMPLE 1)

description: SAMPLE 1

tag: age

value: Young


title: fLow2


title: 4_7H_UcNK_A279_H3_S279 : SS2 sample

value: filtered out of SS2 NK atlas


title: mouse tissue, EPN Sox9-GOF, rep 1

value: brain tumor tissue

value: EPN Sox9-GOF


title: fLow1


title: mouse tissue, EPN control, rep 3

value: control

value: EPN control


title: mouse tissue, EPN Sox9-GOF, rep 3


title: mouse tissue, EPN control, rep 2


title: 204_G13_MHT

value: AB

value: laboratory (reared in aquarium facilities)

value: 90 days old

value: Testis


title: 9_3G_UtrNK_A135_D3_S135 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: fHigh3

value: Formate

value: anode

value: biofilm


title: 204_G13_FLT

value: Ovaries

value: LT


title: 204_G12_FLT


title: microglial cells, APP, Young, male (SAMPLE 2)

description: SAMPLE 2

value: microglial cells

value: 5 days in vitro

value: APP

value: male


title: 11_3E_UcNK_A122_C2_S122 : SS2 sample

value: mouse maternal-fetal interface

value: full length (SS2) scRNa-Seq

value: filtered out of SS2 NK atlas


title: fHigh2


title: mouse tissue, EPN control, rep 1

value: brain tumor tissue

value: control

value: EPN control


title: fHigh1


title: 204_G14_FHT

value: AB

value: laboratory (reared in aquarium facilities)

value: 90 days old

value: HT


title: mouse tissue, HGG Sox9-GOF, rep 2

value: HGG Sox9-GOF


title: 204_G11_MHT

value: Testis


title: mouse tissue, HGG Sox9-GOF, rep 1


title: 11_1i_UcNK_A54_E6_S54 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: Higher3

value: Acetate

value: anode

value: biofilm


title: 9_3G_UtrNK_A186_H6_S186 : SS2 sample


title: mouse tissue, HGG Sox9-LOF, rep 3

value: HGG Sox9-LOF


title: 204_G11_FLT

value: Ovaries

value: LT


title: microglial cells, APP, Aged, female (SAMPLE 30)

description: SAMPLE 30

value: microglial cells

value: 5 days in vitro

value: APP

value: Aged

value: female


title: Higher2


title: mouse tissue, HGG Sox9-LOF, rep 2

value: brain tumor tissue


title: Higher1


title: 204_G10_FLT

value: AB

value: laboratory (reared in aquarium facilities)

value: 90 days old


title: 204_G1_MHT

value: Testis

value: HT


title: 11_1i_UtrNK_A314_C2_S314 : SS2 sample

value: mouse maternal-fetal interface

value: full length (SS2) scRNa-Seq

value: maternal-fetal NK interface atlas (SS2)


title: 11_3E_UtrNK_A268_G4_S268 : SS2 sample


title: ETH015

value: Acetate

value: fumarate

value: biofilm


title: ETH019


title: mouse tissue, HGG Sox9-GOF, rep 3

value: HGG Sox9-GOF


title: mouse tissue, HGG control, rep 3

value: control

value: HGG control


title: 204_G0_MLT

value: LT


title: ETH013


title: 8_1D_UtrNK_A15_B3_S15 : SS2 sample


title: 204_G10_FHT

value: Ovaries


title: ETH018

value: anode


title: 128_G9_FLT

value: AB


title: 9_5B_UcNK_A82_G10_S82 : SS2 sample


title: mouse tissue, HGG Sox9-LOF, rep 1

value: brain tumor tissue

value: HGG Sox9-LOF


title: 9_5B_UcNK_A89_H5_S89 : SS2 sample


title: mouse tissue, HGG control, rep 1


title: 128_G8_FLT

value: laboratory (reared in aquarium facilities)

value: 90 days old


title: 11_1i_UcNK_A27_C3_S27 : SS2 sample

value: mouse maternal-fetal interface


title: 128_G7_FLT


title: ETH008


title: 11_1i_UcNK_A95_H11_S95 : SS2 sample

value: full length (SS2) scRNa-Seq

value: filtered out of SS2 NK atlas


title: 128_G6_MLT

value: Testis


title: mouse tissue, HGG control, rep 2


title: 204_G12_FHT

value: HT


title: ETH010

value: Acetate

value: biofilm


title: ETH005


title: 11_1i_UcNK_A42_D6_S42 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: 128_G6_MHT


title: 9_5B_UtrNK_A260_F8_S260 : SS2 sample


title: 128_G5_MLT


title: 9_5B_UcNK_A24_B12_S24 : SS2 sample


title: 128_G5_MHT


title: ETH003

value: fumarate

value: planktonic


title: 9_5B_UtrNK_A246_E6_S246 : SS2 sample


title: 15_4G_UtrNK_A175_G7_S175 : SS2 sample


title: ETH004


title: ETH002


title: ETH009


title: ETH001


title: 9_3G_UcNK_A311_B11_S311 : SS2 sample


title: 128_G4_MHT


title: 11_1i_UtrNK_A342_E6_S342 : SS2 sample


title: 128_G3_FLT

value: Ovaries

value: LT


title: 11_3E_UcNK_A159_F3_S159 : SS2 sample


title: 15_4G_UcNK_A289_A1_S289 : SS2 sample


title: 128_G22_MLT

value: AB


title: Jurkat, 1D7, dCAS9-KRAB_NT

city: New Haven

first: Jack

middle: Anthony

last: Collora

state: CT

address: 295 Congress Ave

department: Microbial Pathogenesis

institute: Yale University

data_processing:
Reads were trimmed to remove the nextera adapter using cutadapt
Reads were aligned using Bowtie2 to hg38 or NL43-d6-GFP
Mapped reads were filtered for unique alignment, and duplicates were removed
deeptools was used to generate bigwig files for genomic alignment normalized by CPM
CPM scaling factor was extracted and HIV-1 coverage was normalized using R.
Assembly: hg38
Supplementary files format and content: bigWig genomic tracks, CPM normalized
Supplementary files format and content: Wig genomic tracks, CPM normalized

growth_protocol: Cells were maintained at a low density in R10 supplemented puromycin and blasticidin to maintain selection.

extract_protocol:
Cells were transposed as described in Corces et al., Nature Methods 2017.
Resulting DNA was amplified using Nextera primers with cycle number optimized using qPCR to be subsaturating.

tag: cell line

value: Jurkat Cm6


title: Jurkat, 1D7, dCAS9-KRAB_SLTM


title: 128_G21_MLT


title: 128_G20_MLT


title: CD4+_Giant papillae_Human_patient

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

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: Giant papillae

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: Giant papillae

value: Patient


title: 15_4G_UcNK_A332_D8_S332 : SS2 sample

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

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.


title: 128_G4_MLT

value: laboratory (reared in aquarium facilities)

value: 90 days old


title: FUS H517Q MNs (RHB2120)

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt
Trimmed sequence reads were mapped to hg19 using bowtie
Read counts were estimated using R package feature count and normalization were performed using DESeq2
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw readcounts and FPKM values per gene for each Sample

source_name: iPSC

extract_protocol:
RNA was harvested using microRNeasy mini kit (Qiagen).
1.0 ug of total RNA was used to construct of sequencing libraries using the NEBNext Ulltra kit.

value: iPSC

value: iPSC-derived motor neurons

tag: disease state

value: ALS

value: motor neuron differentiation

tag: time

value: Day 30


title: CD45+_Giant papillae_Human_patient

description: 10x Genomics

tag: tissue


title: 128_G2_MLT

value: Testis


title: 11_1i_UtrNK_A358_F10_S358 : SS2 sample

value: mouse maternal-fetal interface

tag: genotype

tag: sample id

value: full length (SS2) scRNa-Seq

value: maternal-fetal NK interface atlas (SS2)


title: CD45+_PBMC_Human_patient

description: 10x Genomics

source_name: PBMC

value: PBMC


title: 128_G2_MHT

tag: strain

tag: FISH origin

value: HT


title: 128_G19_MLT

value: AB

value: LT


title: 9_3G_UcNK_A354_F6_S354 : SS2 sample

tag: mouse id

tag: technology


title: healthy MNs (RHB2117)

value: healthy

tag: treatment


title: Sample_VDJ_Pt1,Pt2,Pt3,Pt4,Pt5,Pt6,Pt7,Pt8,Pt9,Pt10

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: 10x VDJ

data_processing:
Filtered gene expression matrices were generated (for sample 001 and 002 separately) 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 (across sequenced samples 001 and 002, merged) using antibody barcode patterns from TotalSeq.
Mouse specific barcodes were demultiplexed by HTO using Seurat (version 3.2.3).
Assembly: GRCh38 (GENCODE v32/Ensembl 98)

source_name: Sorted CD4+, CD8+, and CD4+CD8+ T cells from patient reseections

extract_protocol:
Cryopreserved melanoma patient samples were individually hash-tagged and CD4+, CD8+ CD4+CD8+ T cells were sorted from each sample. Approximately equal numbers of sorted  cells from each sample were pooled together and labeled with the TotalSeq-C human universal as one sample.
Single-cell transcriptome sequencing  Cryopreserved melanoma patient samples were individually hash-tagged and labeled with the TotalSeq-C human universal cocktail to enable protein detection of genes by cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq). Sorted T cells were stained with Trypan blue and 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 Chip A (10X Genomics PN 230027) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 5,800-7,000 cells with 57% viability proceeded using the Chromium Single Cell 5’ Reagent Kit (10X Genomics PN 1000006) according to the manufacturer’s protocol. cDNA amplification included 13 cycles and 50ng of the material was used to prepare sequencing libraries with 14 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a 28bp/91bp paired end run using the NovaSeq 6000 SP Reagent Kit (100 cycles) (Illumina). An average of 273 million paired reads was generated per sample.         Single-cell V(D)J analysis from RNA  An aliquot of cDNA generated using the methods described above was used to enrich for V(D)J regions using the Chromium Single Cell V(D)J Enrichment Kit Human T Cell (10X Genomics PN 1000005) according to the manufacturer’s protocol with 10 cycles of PCR during enrichment and 9 cycles during library preparation. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a 150bp/150bp paired end run using the NovaSeq 6000 S4 Reagent Kit (300 cycles) (Illumina). An average of 107 million paired reads was generated per sample.
scRNA/TCR sequencing with hasthtag and feature barcoding

value: Tumor infiltrating T cells

tag: gender

value: F,M,F,F,M,M,F,F,M,F

tag: disease stage

value: IV,IIB,IIID,IIIC,IV,IIIB,IV,IV,IIC,IV

tag: response

tag: dnaid

tag: barcode


title: 128_G19_MHT

value: laboratory (reared in aquarium facilities)

tag: age

value: 90 days old


title: FUS H517Q MNs (RHB2115)

tag: cell line

value: iPSC

tag: cell type

value: iPSC-derived motor neurons

value: ALS


title: 4_7H_UtrNK_A40_D4_S40 : SS2 sample

city: Oxford

first: Gurman

last: Kaur

address: Headley Way

institute: University of Oxford

tag: atlas


title: Sample_RNA_Pt1,Pt2,Pt3,Pt4,Pt5,Pt6,Pt7,Pt8,Pt9,Pt10

description: 10x scRNA


title: 11_1i_UtrNK_A330_D6_S330 : SS2 sample

tag: tissue


title: healthy MNs (RHB2112)

tag: disease state

value: motor neuron differentiation

tag: time

value: Day 30


title: 128_G17_MHT

tag: strain

value: Testis


title: 8_1D_UtrNK_A19_B7_S19 : SS2 sample

value: mouse maternal-fetal interface

tag: genotype

tag: sample id

value: full length (SS2) scRNa-Seq

value: maternal-fetal NK interface atlas (SS2)


title: 128_G18_MLT

value: AB

tag: FISH origin


title: 128_G17_FLT

value: Ovaries

tag: treatment

value: LT


title: CLL cells from patient 4 cultured on 3T40 for 48 hours

city: Amsterdam

first: Fleur

last: Peters

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC (AMC)

data_processing:
Sequence quality was assessed with FastQC, raw FASTq files were aligned with hisat2.1.0
Counts file is output of hisat
Assembly: GRCh38/hg38
Supplementary files format and content: raw counts in comma-delimited format

source_name: Blood PBMCs

extract_protocol:
Total RNA was extracted with the Qiagen Mini kit
KAPA mRNA Hyperprep
mRNA sequencing on Illumina HiSeq 4000

value: Blood PBMCs

value: B cells

tag: gender

value: Female

tag: mutation status

value: Mutated

value: 48 hours


title: CLL cells from patient 3 cultured on 3T40 for 48 hours


title: Sample_HTO_Pt1,Pt2,Pt3,Pt4,Pt5,Pt6,Pt7,Pt8,Pt9,Pt10

description: 10x HTO

value: Tumor infiltrating T cells

value: F,M,F,F,M,M,F,F,M,F

tag: disease stage

value: IV,IIB,IIID,IIIC,IV,IIIB,IV,IV,IIC,IV

tag: response


title: CLL cells from patient 2 cultured on 3T40 for 48 hours

value: Unmutated


title: 128_G16_MLT

value: laboratory (reared in aquarium facilities)

value: 90 days old


title: CLL cells from patient 1 cultured on 3T40 for 48 hours

value: Male


title: 15_4G_UcNK_A291_A3_S291 : SS2 sample

value: mouse maternal-fetal interface

tag: mouse id

tag: technology

value: full length (SS2) scRNa-Seq


title: 4_7H_UtrNK_A2_A2_S2 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: ChAd_ChAd_2_Day7

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:
Raw sequencing data was aligned using Cellranger (version 5.0).
The quality control, normalization, dimension reduction, cell clusters, UMAP projection, and cell type annotation were performed using Seurat (version 4.0).
Assembly: GRCh38

source_name: PBMCs

growth_protocol: Single-cell suspensions were then immediately loaded on the 10X Genomics Chromium Controller with a loading target of 20,000 cells.

extract_protocol: The downstream library constructions were performed using the Chromium Next GEM Single Cell 3′ Kit v3.1 (Dual Index) according to the manufacturer’s instructions (10x Genomics).

tag: vaccine

value: PBMCs


title: ChAd_ChAd_1_Day7

tag: cell type


title: ChAd_ChAd_1_Day1


title: ChAd_ChAd_2_Day1


title: 128_G15_MHT

value: AB

tag: age

value: Testis

value: HT


title: 11_1i_UtrNK_A310_B10_S310 : SS2 sample

tag: tissue

tag: atlas


title: CLL cells from patient 4 cultured on 3T3 for 48 hours

value: Blood PBMCs

value: B cells

value: Female

tag: time


title: ChAd_BNT_2_Day7


title: 128_G14_MHT

tag: strain


title: CLL cells from patient 3 cultured on 3T3 for 48 hours

value: Mutated

value: 48 hours


title: ChAd_BNT_2_Day1


title: 128_G15_FLT

value: Ovaries

value: LT


title: 9_3G_UcNK_A304_B4_S304 : SS2 sample

tag: genotype


title: 8_1D_UcNK_A243_E3_S243 : SS2 sample

tag: sample id


title: 15_4G_UtrNK_A141_D9_S141 : SS2 sample


title: 9_5B_UtrNK_A233_D5_S233 : SS2 sample


title: ChAd_BNT_1_Day7


title: 128_G14_FLT

tag: FISH origin

value: laboratory (reared in aquarium facilities)


title: BNT_BNT_2_Day7


title: 11_1i_UcNK_A81_G9_S81 : SS2 sample


title: CLL cells from patient 1 cultured on 3T3 for 48 hours

value: Unmutated

tag: treatment


title: 128_G12_MHT

value: 90 days old


title: ChAd_BNT_1_Day1


title: 11_1i_UtrNK_A368_G8_S368 : SS2 sample

value: mouse maternal-fetal interface


title: MG1655-WT-TR1

city: Freiburg

first: Florian

last: Eggenhofer

address: Georges Köhler Allee 106

department: Institute for Informatics

institute: University of Freiburg

data_processing:
Basecalling was performed with RTAVersion 2.4.11
Demultiplexing with bcl2fastq v2.20.0.422
Trimming performed with cutadapt version 2.1
rRNA filtering with SortMeRNA 2.1
Mapping with segemehl 3.4
Coverage file creation with Reademption
Genome_build: ASM584v2
Supplementary_files_format_and_content: wig files were generated in Reademption single nucleotide mapping style and converted to bigwig

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli K-12 substr. MG1655 cells

growth_protocol: LB broth log phase

extract_protocol:
hot phenol
Dual adaptor ligation sRNA protocol

tag: genotype/variation

value: wildtype


title: 128_G12_FLT


title: 128_G13_MHT


title: ChAd-44_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

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: gender

value: 2nd dose, ChAdOx1


title: MG1655-WT-RBP1

data_processing:
Library strategy: Ribo-seq
Basecalling was performed with RTAVersion 2.4.11
Demultiplexing with bcl2fastq v2.20.0.422
Trimming performed with cutadapt version 2.1
rRNA filtering with SortMeRNA 2.1
Mapping with segemehl 3.4
Coverage file creation with Reademption
Genome_build: ASM584v2
Supplementary_files_format_and_content: wig files were generated in Reademption single nucleotide mapping style and converted to bigwig

treatment_protocol: chloramphenicol/monosome isolation


title: Tonsil_20um

first: Yanxiang

last: Deng

address: 55 Prospect Street

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: Human tonsil

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: Tonsil

tag: spatial resolution

value: 20 um


title: 11_1i_UcNK_A18_B6_S18 : SS2 sample

value: full length (SS2) scRNa-Seq

value: maternal-fetal NK interface atlas (SS2)


title: 4_7H_UtrNK_A76_G4_S76 : SS2 sample


title: BNT_BNT_2_Day1

value: PBMCs


title: 9_3G_UtrNK_A126_C6_S126 : SS2 sample


title: CLL cells from patient 2 cultured on 3T3 for 48 hours

value: Blood PBMCs

value: B cells

tag: mutation status


title: BNT_BNT_1_Day7


title: 128_G13_MLT

value: AB

value: Testis


title: MG1655-WT-S400-RBP1


title: 11_3E_UcNK_A113_B5_S113 : SS2 sample

tag: mouse id

value: filtered out of SS2 NK atlas


title: BNT_BNT_1_Day1


title: 4_7H_UtrNK_A10_A10_S10 : SS2 sample

tag: technology


title: ChAd-44_II-D0

value: Female

tag: vaccine


title: 9_5B_UcNK_A32_C8_S32 : SS2 sample


title: 128_G11_MLT

value: laboratory (reared in aquarium facilities)

value: LT


title: P9 - ATAC-Seq - Tumor Pmel CD8+CD4+

data_processing: ATAC-seq data were aligned to the mm9 reference genome. Alignment and peak calling were performed by atac-seq-pipeline v1.7.1 from ENCODE Data Coordination Center (ENCODE DCC).

source_name: Sorted T cells

growth_protocol: B16F10 melanoma cells (2x105 cells) were implanted subcutaneously in 0.2ml of matrigel.  Tumors were resected 11 days after T cell transfer and TRP1 (CD45.1) CD4+ and CD4+CD8+, and Pmel (CD90.1) CD8+ and CD8+CD4+ TILS were FACs sorted. Naïve Trp1 CD4+ and Pmel CD8+ T cells were sorted directly from the spleen of naive transgenic mice.

extract_protocol:
Samples were isolated from 3 independent experiments of pooled spleens (n=3) or tumors (n=5-8) as follows: (i)Naïve TRP1 CD4+ T cells and naïve PMEL CD8+ T cells were sorted by flow cytometry from spleens of Trp1 and Pmel-1 transgenic mice. (ii) TRP1 CD4+ and TRP1 CD4+CD8+ were sorted from B16 tumors of C57BL/6 mice that had been adoptively transferred with naïve TRP1 CD4+ T cells 11 days prior. (iii) PMEL CD8+ and PMEL CD4+CD8+ were sorted from B16 tumors of C57BL/6 mice that had been adoptively transferred with naïve PMEL CD8+ T cells 11 days prior. Cells were gated on congenic labels (TRP1 – CD45.1, PMEL - CD90.1), CD3+, CD4+CD8- (TRP1), CD4+CD8+ (TRP1 and PMEL), or CD4-CD8+ (PMEL). Samples were directly sorted into Trizol (Invitrogen), adjusted to 500uL total volume and frozen and stored at −80 °C. After flow-sorting, all samples for downstream ATAC-seq analysis were frozen in 10% DMSO and stored at −80 °C.
Profiling of chromatin was performed by ATAC-seq as described by Buenrostro, et al34. Briefly, 8-50,000 viably frozen T cells were thawed, washed in cold PBS, and lysed. The transposition reaction containing TDE1 Tagment DNA Enzyme (Illumina catalog # 20034198) was incubated at 37°C for 30 minutes. The DNA was cleaned with the MinElute PCR Purification Kit (QIAGEN catalog # 28004) and material was amplified for 5 cycles using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs catalog # M0541L). After evaluation by real-time PCR, 7-13 additional PCR cycles were done. The final product was cleaned by aMPure XP beads (Beckman Coulter catalog # A63882) at a 1X ratio, and size selection was performed at a 0.5X ratio. Libraries were sequenced on a HiSeq4000 in a PE50 run, using the HiSeq 3000/4000 SBS Kit (Illumina). An average of 57 million paired reads were generated per 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 or PMEL CD8+ T cells were intravenously injected into the tail vein in 100ul PBS.

tag: tumor or no tumor

value: Tumor

tag: sorted t cell population

value: No treatment

value: B6.Cg-Thy1a/Cy Tg(TcraTcrb)8Rest/J


title: 128_G10_FLT

tag: age

value: 90 days old

tag: tissue

value: Ovaries


title: ChAd-44_II-D2

value: 2nd dose, ChAdOx1

tag: cell type


title: 9_3G_UcNK_A329_D5_S329 : SS2 sample

value: mouse maternal-fetal interface

value: full length (SS2) scRNa-Seq

tag: atlas


title: ChAd-43_II-D8

value: PBMCs


title: P7 - ATAC-Seq - Tumor Pmel CD8+CD4+

tag: strain


title: P8 - ATAC-Seq - Tumor Pmel CD8+CD4+


title: 128_G1_MHT

value: HT


title: 128_G10_MHT


title: 128_G1_MLT


title: 11_1i_UtrNK_A306_B6_S306 : SS2 sample

tag: genotype

tag: sample id

value: maternal-fetal NK interface atlas (SS2)


title: ChAd-43_II-D2


title: P6 - ATAC-Seq - Tumor Pmel CD8+

tag: treatment


title: 8_1D_UtrNK_A4_A4_S4 : SS2 sample


title: 191118-99-WT-6hr-S25

city: LA JOLLA

first: Sahar

last: Taheri

state: California

address: 9500 GILMAN DR.

institute: UCSD

data_processing:
RNASeq data was processed using kallisto (version 0.45.0). Gene-level TPM values and gene annotations were computed using a custom Perl Script.
Assembly: Mus_musculus genome build GRCm38.94
Supplementary files format and content: tab-delimited text file includes log2 of TPM values

source_name: Peritoneal macrophage

extract_protocol:
Upon treatement total RNA was isolated using TRIzol reagent (Life Technologies) and Quick-RNA MiniPrep Kit (Zymo Research, USA) as per manufacturer’s guidelines.
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: Murine peritoneal macrophage were isolated from macrophage specific GIV knockout mice and their littermate WT controls 4 days after thiglycollate injection (IP). Peritoneal macrophage were stimulated or not with 100ng/ml of LPS for 6h.

value: Peritoneal macrophage

value: WT

value: LPS 6h


title: ChAd-39_I-D7

value: Female

value: 1st dose, ChAdOx1


title: 9_3G_UcNK_A356_F8_S356 : SS2 sample

value: filtered out of SS2 NK atlas


title: 9_5B_UcNK_A53_E5_S53 : SS2 sample


title: 191127-88-KO-6hr-S27

value: macrophage specific GIV KO


title: ChAd-39_I-D0


title: P4 - ATAC-Seq - Tumor Pmel CD8+

value: Tumor

value: No treatment


title: 191118-88-KO-6hr-S27


title: 4_7H_UtrNK_A95_H11_S95 : SS2 sample


title: ChAd-38_I-D7


title: 191127-99-WT-0-S20


title: P2 - ATAC-Seq - Naïve Pmel CD8+

value: No Tumor

value: B6.Cg-Thy1a/Cy Tg(TcraTcrb)8Rest/J


title: 191118-916-WT-0-S21


title: P3 - ATAC-Seq - Naïve Pmel CD8+


title: P1 - ATAC-Seq - Naïve Pmel CD8+


title: 15_4G_UcNK_A359_F11_S359 : SS2 sample


title: ChAd-38_I-D2


title: 191118-88-KO-0-S22


title: 4_7H_UcNK_A216_B12_S216 : SS2 sample


title: ChAd-37_I-D3


title: P5 - ATAC-Seq - Tumor Pmel CD8+


title: ChAd-37_I-D7


title: 191127-916-KO-6hr-S29


title: 191127-88-KO-0-S22


title: ChAd-38_I-D0


title: T9 - ATAC-Seq - Tumor Trp1 CD4+CD8+

value: RAG1- BW TRP-1 TCR


title: ChAd-37_I-D0


title: T8 - ATAC-Seq - Tumor Trp1 CD4+CD8+


title: T6 - ATAC-Seq - Tumor Trp1 CD4+


title: 9_5B_UcNK_A42_D6_S42 : SS2 sample

value: mouse maternal-fetal interface


title: 15_4G_UcNK_A319_C7_S319 : SS2 sample

value: full length (SS2) scRNa-Seq


title: 11_1i_UcNK_A78_G6_S78 : SS2 sample


title: 191127-99-KO-6hr-S28


title: ChAd-36_I-D2

value: PBMCs


title: ChAd-36_I-D0


title: T7 - ATAC-Seq - Tumor Trp1 CD4+CD8+


title: ChAd-36_I-D7


title: 11_3E_UcNK_A126_C6_S126 : SS2 sample


title: 191118-88-WT-6hr-S24


title: T5 - ATAC-Seq - Tumor Trp1 CD4+


title: 191118-916-WT-6hr-S26


title: 191127-916-WT-0-S21


title: 8_1D_UcNK_A202_A10_S202 : SS2 sample


title: 191127-99-KO-0-S23


title: T2 - ATAC-Seq - Naïve Trp1 CD4+


title: ChAd-35_I-D7


title: 9_3G_UcNK_A302_B2_S302 : SS2 sample


title: T3 - ATAC-Seq - Naïve Trp1 CD4+


title: T4 - ATAC-Seq - Tumor Trp1 CD4+


title: 11_1i_UtrNK_A305_B5_S305 : SS2 sample


title: T1 - ATAC-Seq - Naïve Trp1 CD4+


title: 191118-99-KO-6hr-S28


title: ChAd-35_I-D0


title: P9 - Tumor Pmel CD8+CD4+

data_processing:
Bulk RNAseq for each sample (FASTQ) were aligned to corresponding genome with STAR (v2.6.0)
Count based expression profiles were quantified using Subread featureCounts (v1.5.1)
Assembly: mm10 (GRCm38.75)

extract_protocol:
Samples were isolated from 3 independent experiments of pooled spleens (n=3) or tumors (n=5-8) as follows: (i)Naïve TRP1 CD4+ T cells and naïve PMEL CD8+ T cells were sorted by flow cytometry from spleens of Trp1 and Pmel-1 transgenic mice. (ii) TRP1 CD4+ and TRP1 CD4+CD8+ were sorted from B16 tumors of C57BL/6 mice that had been adoptively transferred with naïve TRP1 CD4+ T cells 11 days prior. (iii) PMEL CD8+ and PMEL CD4+CD8+ were sorted from B16 tumors of C57BL/6 mice that had been adoptively transferred with naïve PMEL CD8+ T cells 11 days prior. Cells were gated on congenic labels (TRP1 – CD45.1, PMEL - CD90.1), CD3+, CD4+CD8- (TRP1), CD4+CD8+ (TRP1 and PMEL), or CD4-CD8+ (PMEL). Samples were directly sorted into Trizol (Invitrogen), adjusted to 500uL total volume and frozen and stored at −80 °C. RNA was extracted using RNeasy mini kit (Qiagen) per instructions provided by the manufacturer.
After ribogreen quantification and quality control of Agilent BioAnalyzer, total RNA underwent amplification using the SMART-seq V4 (Clonetech) ultralow input RNA kit for sequencing (12 cycles of amplification for 2–10 ng of total RNA). Subsequently, 10 ng of amplified cDNA was used to prepare Illumina Hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems). Samples were run on a Hiseq 4000, in a 50-bp/50-bp paired-end run, using the TruSeq SBS Kit v3 (Illumina).


title: ChAd-34_I-D7

value: Male


title: ChAd-34_I-D2


title: P8 - Tumor Pmel CD8+CD4+


title: 191118-88-WT-0-S19


title: 11_3E_UcNK_A140_D8_S140 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: 11_3E_UcNK_A181_H1_S181 : SS2 sample


title: 191127-88-WT-0-S19

value: Peritoneal macrophage


title: 9_3G_UcNK_A345_E9_S345 : SS2 sample


title: 191127-916-WT-6hr-S26

value: WT


title: 8_1D_UcNK_A252_E12_S252 : SS2 sample


title: ChAd-34_I-D0


title: ChAd-33_I-D7


title: P6 - Tumor Pmel CD8+


title: ChAd-35_I-D2


title: 191127-88-WT-6hr-S24

value: LPS 6h


title: 4_7H_UcNK_A258_F6_S258 : SS2 sample


title: 191118-916-KO-6hr-S29


title: 191127-99-WT-6hr-S25


title: 9_3G_UtrNK_A98_A2_S98 : SS2 sample


title: P5 - Tumor Pmel CD8+


title: 15_4G_UcNK_A326_D2_S326 : SS2 sample


title: ChAd-33_I-D0

value: Female


title: 8_1D_UcNK_A276_G12_S276 : SS2 sample


title: ChAd-32_I-D7

value: 1st dose, ChAdOx1


title: P3 - Naïve Pmel CD8+


title: P2 - Naïve Pmel CD8+


title: 191118-99-WT-0-S20


title: P4 - Tumor Pmel CD8+


title: 9_3G_UcNK_A371_G11_S371 : SS2 sample


title: ChAd-32_I-D0


title: P7 - Tumor Pmel CD8+CD4+


title: P1 - Naïve Pmel CD8+


title: ChAd-31_I-D7


title: ChAd-31_I-D3


title: DMSOd4_1

first: Ellen

last: Busschers

state: Texas

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.

tag: cell line

value: stromal cells

value: DMSO control for ML-60218

value: osteoblast differentiation


title: T9 - Tumor Trp1 CD4+CD8+

value: Tumor

value: No treatment


title: ML_d4_3

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


title: ChAd-32_I-D2

tag: gender


title: DMSOd4_2


title: T8 - Tumor Trp1 CD4+CD8+

value: RAG1- BW TRP-1 TCR


title: 9_5B_UtrNK_A265_G1_S265 : SS2 sample

value: mouse maternal-fetal interface


title: 15_4G_UtrNK_A97_A1_S97 : SS2 sample

value: full length (SS2) scRNa-Seq

value: filtered out of SS2 NK atlas


title: ChAd-33_I-D2

value: PBMCs


title: ML_d4_2


title: ChAd-31_I-D0


title: DMSOd4_3


title: 11_3E_UcNK_A123_C3_S123 : SS2 sample


title: 11_1i_UtrNK_A332_D8_S332 : SS2 sample

value: maternal-fetal NK interface atlas (SS2)


title: T7 - Tumor Trp1 CD4+CD8+


title: T6 - Tumor Trp1 CD4+


title: ML_d4_1


title: 11_3E_UcNK_A186_H6_S186 : SS2 sample


title: pIndd4_3

value: empty control for MAF1 overexpression


title: 15_4G_UtrNK_A145_E1_S145 : SS2 sample


title: T5 - Tumor Trp1 CD4+


title: 15_4G_UcNK_A372_G12_S372 : SS2 sample


title: ChAd-30_I-D0

value: Male


title: pIndd4_1


title: ChAd-29_I-D7


title: 11_3E_UcNK_A168_F12_S168 : SS2 sample


title: T4 - Tumor Trp1 CD4+


title: T2 - Naïve Trp1 CD4+

value: No Tumor


title: MAF1d4_3

value: MAF1 overexpression


title: T3 - Naïve Trp1 CD4+


title: T1 - Naïve Trp1 CD4+


title: MAF1d4_2


title: ChAd-29_I-D0

value: Female

value: 1st dose, ChAdOx1


title: ChAd-29_I-D2


title: 15_4G_UcNK_A370_G10_S370 : SS2 sample


title: ChAd-28_I-D7


title: SCRBd4_3

value: stromal cells

value: scramble control for shBrf1


title: MAF1d4_1

value: osteoblast differentiation


title: ChAd-30_I-D7


title: pIndd4_2


title: CMU2-164-16

city: Charlottesville

first: Clint

last: Upchurch

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

state: VA

address: 1307 Lane Rd.

department: Pharmacology

institute: University of Virginia

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.

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.

value: Hepatocytes

value: OxPAPC


title: ChAd-30_I-D2


title: ChAd-28_I-D2


title: 15_4G_UtrNK_A152_E8_S152 : SS2 sample


title: CMU2-164-15


title: SCRBd4_2


title: ChAd-28_I-D0