title: HCC15, sgBIRC6-4, rep 2

city: Cambridge

first: Tsukasa

last: Shibue

state: MA

department: Cancer Program

institute: Broad Institute of MIT and Harvard

description:
1_HCC15_sgBIRC6-4B_H2LK3BGX9
2_HCC15_sgBIRC6-4B_H2LK3BGX9
3_HCC15_sgBIRC6-4B_H2LK3BGX9
4_HCC15_sgBIRC6-4B_H2LK3BGX9

data_processing:
RNA-seq reads were aligned to the GRCh37 build of the human genome reference using STAR 2.4.2a.
The GENCODE v19 annotation was used for the STAR alignment and all other quantifications.
Gene level read count values were calculated using RNA-SeQC v1.1.8.
Isoform-level expression in TPM (transcripts per million) was quantified using RSEM v.1.2.22.
Assembly: GRCh37/hg19
Supplementary files format and content: Tab-delimited text files including TPM values for each replicate Sample [BIRC6_RNAseq.rsem_transcripts_tpm.txt.gz]
Supplementary files format and content: Tab-delimited text files including gene-level logCPM values after collapsing the replucates [BIRC6_rep_collapsed_logCPM.txt.gz]
Supplementary files format and content: Tab-delimited text files including differential expression (logFC) of the genes between control (sgCh2-2) and BIRC6 KO samples in each cell line and the statistical significance of the diffference [BIRC6_DE_sgCh2-2_vs_sgBIRC6.txt.gz]

source_name: lung

growth_protocol: All the cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol:
All the cells were engineered to constitutively express Cas9.  These cells were subsequently transduced with an sgRNA against BIRC6 (sgBIRC6-1, -4; two different sgRNA sequences against BIRC6 were tested) or a control sgRNA (sgCh2-2).
Cells were harvested for RNA extraction four days after the transduction of an sgRNA

value: lung

tag: cell line

value: lung cance cells

value: BIRC6 KO


title: HCC15, sgBIRC6-4, rep 1

status: Public on Dec 21 2022

type: SRA

country: USA

description:
1_HCC15_sgBIRC6-4A_H2LK3BGX9
2_HCC15_sgBIRC6-4A_H2LK3BGX9
3_HCC15_sgBIRC6-4A_H2LK3BGX9
4_HCC15_sgBIRC6-4A_H2LK3BGX9

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: HCC15, sgBIRC6-1, rep 2

description:
1_HCC15_sgBIRC6-1B_H2LK3BGX9
2_HCC15_sgBIRC6-1B_H2LK3BGX9
3_HCC15_sgBIRC6-1B_H2LK3BGX9
4_HCC15_sgBIRC6-1B_H2LK3BGX9


title: IH20

type: RNA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Agilent miRNA hybridization protocol

scan_protocol: Standard Agilent scanning protocol

data_processing: The data were processed and normalised using the Bioconductor  AgiMicroRna implementation in R

source_name: FFPE

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Agilent MicroRNA Expression Profiling Assay Guide).

extract_protocol: RNA was extracted with FFPE miRNeasy kit in accordance with manufacture's protocol (QIAGEN).

tag: age

tag: grading

tag: Stage

value: IC

tag: histotype

value: serous

tag: disease state

value: early stage ovarian cancer


title: JNKKO-BBTGF1 [RNA-seq]

city: Worcester

first: Zeynep

last: Itah

address: 373 Plantation St. Suite 309

department: Program in Molecular Medicine

institute: UMass Medical School

data_processing:
Sequenced reads were trimmed for adaptor and low quality sequences using cutadapt
Clean reads were then mapped to hg38 genome using RSEM
TPM and Counts were calculated using RSEM
Genome_build: hg38
Supplementary_files_format_and_content: tab separated files include read count values for each Sample
Supplementary_files_format_and_content: tab separated files include TPM values for each Sample

source_name: Mammary epithelial cell line

growth_protocol: Cells (2-2.5x10^6) were routinely cultured in growth media containing DMEM:F12 with 5% horse serum, EGF, insulin, hydrocortizone, cholera toxin and penicillin and streptomycin. Cells were splitted within 2-3 days.

extract_protocol:
Acini structures  were removed from GFR- matrigel using cell recovery solution on ice and total RNA was harvested using miRNeasy kit with Dnase I treatment (QIAGEN# 217084).
mRNAs were enriched using oligo(dT) beads. After rRNA depletion using Ribo-Zero kit, mRNA was fragmented randomly, and cDNA was synthesized with random hexamer primers. After second strand synthesis, terminal repair, A ligation and adaptor ligation was performed. Following to size selection and PCR enrichment, cDNA libraries were pair end sequenced for 150bp on NovaSeq6000  platform.

treatment_protocol: For the experiment, cells were grown on growth factor reduced(GFR) matrigel within assay media ( DMEM/F12 supplemented with 2% donor horse serum and insulin,  cholera toxin, hydrocortisone,  penicillin and streptomycin). On day 7, EGF replaced with Ethanol (control) or B/B homodimerizer with or without TGF-β1 for 14 days.

tag: cell line background

value: JNK knockout

value: B/B homodimerizer+TGF-β1

tag: time

value: 21 days= 7+14day with treatments


title: IG83

value: IIB


title: IG82

value: endometroid


title: G075_O04_CyCMV_36958_BD1_RNA_mRNAseq_run09_S12

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

data_processing:
Read quality for each sample was first assessed with FASTQC
Residual adapters were removed with trim galore. Globin and rRNA reads were filtered out using bowtie2.
Remaining reads were alligned to the Macaca mulatta genome using STAR version 2.7.5
Gene counts were calculated with HTSeq-count version 0.12
Genes with counts less than 10 averaged across all samples were filtered out. The filtered count matrix then underwent TMM normalization followed by voom transformation.
Assembly: Mmul10, Ensembl v100
Supplementary files format and content: Normalized Count Matrix

organism: Macaca fascicularis

extract_protocol:
RNA was extracted using the RNAdvance Blood Kit from Beckman Coulter
mRNA-seq libraries were constructed using KAPA RNA HyperPrep kit with RIboErase (HMR) Globin in conjunction with the KAPA mRNA Capture kit by Roche.
Libraries were sequenced on an Illumina NextSeq500 sequencer using Illumina NextSeq 500/550 High Output v2 kits (150 cycles) following the manufacturer's protocol for sample handling and loading.

tag: age (years)

tag: group

value: Boost

tag: outcome

value: Unprotected

tag: time point

tag: Sex

value: M

value: Whole Blood


title: JNKKO-BB3 [RNA-seq]

value: B/B homodimerizer


title: HCC15, sgBIRC6-1, rep 1

description:
1_HCC15_sgBIRC6-1A_H2LK3BGX9
2_HCC15_sgBIRC6-1A_H2LK3BGX9
3_HCC15_sgBIRC6-1A_H2LK3BGX9
4_HCC15_sgBIRC6-1A_H2LK3BGX9

tag: cell line


title: HCC15, sgCh2-2, rep 2

description:
1_HCC15_sgCh2-2B_H2LK3BGX9
2_HCC15_sgCh2-2B_H2LK3BGX9
3_HCC15_sgCh2-2B_H2LK3BGX9
4_HCC15_sgCh2-2B_H2LK3BGX9

tag: tissue

value: control sgRNA


title: G073_O04_CyCMV_36953_BD1_RNA_mRNAseq_run08_S14

value: Protected


title: JNKKO-BB2 [RNA-seq]


title: HCC15, sgCh2-2, rep 1

description:
1_HCC15_sgCh2-2A_H2LK3BGX9
2_HCC15_sgCh2-2A_H2LK3BGX9
3_HCC15_sgCh2-2A_H2LK3BGX9
4_HCC15_sgCh2-2A_H2LK3BGX9

value: lung

tag: cell type

value: lung cance cells


title: JNKKO-BB1 [RNA-seq]

tag: genotype


title: JNKKO-Cntrl3 [RNA-seq]

tag: treatment

value: Control


title: G072_O04_CyCMV_36959_BD0_RNA_mRNAseq_run11_S4


title: G071_O04_CyCMV_36958_BD0_RNA_mRNAseq_run10_S15


title: II50

tag: age

value: IA


title: SW837, sgBIRC6-4, rep 2

description:
1_SW837_sgBIRC6-4B_H2LK3BGX9
2_SW837_sgBIRC6-4B_H2LK3BGX9
3_SW837_sgBIRC6-4B_H2LK3BGX9
4_SW837_sgBIRC6-4B_H2LK3BGX9

source_name: colon

value: colon

value: colorectal cancer cells

value: BIRC6 KO


title: SW837, sgBIRC6-4, rep 1

description:
1_SW837_sgBIRC6-4A_H2LK3BGX9
2_SW837_sgBIRC6-4A_H2LK3BGX9
3_SW837_sgBIRC6-4A_H2LK3BGX9
4_SW837_sgBIRC6-4A_H2LK3BGX9


title: IJ01

tag: grading

value: IC

value: early stage ovarian cancer


title: JNKKO-Cntrl2 [RNA-seq]

value: JNK knockout

value: 21 days= 7+14day with treatments


title: IH18

tag: Stage

value: clear cells


title: IG74

value: IIA

tag: histotype

value: serous


title: SW837, sgBIRC6-1, rep 2

description:
1_SW837_sgBIRC6-1B_H2LK3BGX9
2_SW837_sgBIRC6-1B_H2LK3BGX9
3_SW837_sgBIRC6-1B_H2LK3BGX9
4_SW837_sgBIRC6-1B_H2LK3BGX9


title: G070_O04_CyCMV_36957_BD0_RNA_mRNAseq_run07_S12

value: Boost

value: M

value: Whole Blood


title: G069_O04_CyCMV_36953_BD0_RNA_mRNAseq_run07_S3

value: Protected


title: SW837, sgBIRC6-1, rep 1

description:
1_SW837_sgBIRC6-1A_H2LK3BGX9
2_SW837_sgBIRC6-1A_H2LK3BGX9
3_SW837_sgBIRC6-1A_H2LK3BGX9
4_SW837_sgBIRC6-1A_H2LK3BGX9


title: WT-BBTGF3 [RNA-seq]

value: B/B homodimerizer+TGF-β1


title: JNKKO-Cntrl1 [RNA-seq]

value: Control


title: G074_O04_CyCMV_36957_BD1_RNA_mRNAseq_run10_S6


title: IG75

tag: disease state


title: WT-BBTGF2 [RNA-seq]

tag: cell line background

value: Wild type


title: IG73

value: IA


title: G068_O04_CyCMV_36959_D1_RNA_mRNAseq_run12_S28

value: Prime

value: Unprotected


title: G067_O04_CyCMV_36958_D1_RNA_mRNAseq_merged


title: IH19

value: IC

value: mucinous


title: WT-BBTGF1 [RNA-seq]

tag: time


title: G066_O04_CyCMV_36957_D1_RNA_mRNAseq_run12_S20

tag: age (years)


title: WT-BB3 [RNA-seq]

value: B/B homodimerizer


title: G065_O04_CyCMV_36953_D1_RNA_mRNAseq_run12_S21

tag: group


title: IJ36

value: endometroid

value: early stage ovarian cancer


title: G064_O04_CyCMV_36490_DX2_RNA_mRNAseq_run12_S29

tag: outcome

value: F


title: WT-BB2 [RNA-seq]

value: 21 days= 7+14day with treatments


title: WT-BB1 [RNA-seq]


title: G063_O04_CyCMV_36485_DX2_RNA_mRNAseq_run10_S12

value: Boost

tag: time point


title: SW837, sgCh2-2, rep 2

description:
1_SW837_sgCh2-2B_H2LK3BGX9
2_SW837_sgCh2-2B_H2LK3BGX9
3_SW837_sgCh2-2B_H2LK3BGX9
4_SW837_sgCh2-2B_H2LK3BGX9

value: colon

value: colorectal cancer cells

value: control sgRNA


title: IG72

value: IIB

value: serous


title: WT-Cntrl3 [RNA-seq]

value: Wild type

value: Control


title: JIMT1, sgBIRC6-1, rep 2

description:
1_JIMT1_sgBIRC6-1B_H2LK3BGX9
2_JIMT1_sgBIRC6-1B_H2LK3BGX9
3_JIMT1_sgBIRC6-1B_H2LK3BGX9
4_JIMT1_sgBIRC6-1B_H2LK3BGX9

source_name: breast

value: breast

value: breast cancer cells

value: BIRC6 KO


title: JIMT1, sgBIRC6-1, rep 1

description:
1_JIMT1_sgBIRC6-1A_H2LK3BGX9
2_JIMT1_sgBIRC6-1A_H2LK3BGX9
3_JIMT1_sgBIRC6-1A_H2LK3BGX9
4_JIMT1_sgBIRC6-1A_H2LK3BGX9


title: G062_O04_CyCMV_36480_DX2_RNA_mRNAseq_run07_S6

value: Protected

tag: Sex

value: Whole Blood


title: IJ00

value: IA


title: IH56

value: endometroid

value: early stage ovarian cancer


title: IG71


title: WT-Cntrl2 [RNA-seq]

value: 21 days= 7+14day with treatments


title: IJ23


title: SW837, sgCh2-2, rep 1

description:
1_SW837_sgCh2-2A_H2LK3BGX9
2_SW837_sgCh2-2A_H2LK3BGX9
3_SW837_sgCh2-2A_H2LK3BGX9
4_SW837_sgCh2-2A_H2LK3BGX9

tag: cell line


title: G061_O04_CyCMV_36479_DX2_RNA_mRNAseq_run10_S11

value: Boost

value: Unprotected

value: F

tag: tissue


title: JIMT1, sgCh2-2, rep 2

description:
1_JIMT1_sgCh2-2B_H2LK3BGX9
2_JIMT1_sgCh2-2B_H2LK3BGX9
3_JIMT1_sgCh2-2B_H2LK3BGX9
4_JIMT1_sgCh2-2B_H2LK3BGX9

tag: cell type

value: control sgRNA


title: WT-Cntrl1 [RNA-seq]

tag: genotype


title: JIMT1, sgBIRC6-4, rep 2

description:
1_JIMT1_sgBIRC6-4B_H2LK3BGX9
2_JIMT1_sgBIRC6-4B_H2LK3BGX9
3_JIMT1_sgBIRC6-4B_H2LK3BGX9
4_JIMT1_sgBIRC6-4B_H2LK3BGX9

tag: treatment


title: G060_O04_CyCMV_36490_BD7_RNA_mRNAseq_merged


title: JIMT1, sgBIRC6-4, rep 1

description:
1_JIMT1_sgBIRC6-4A_H2LK3BGX9
2_JIMT1_sgBIRC6-4A_H2LK3BGX9
3_JIMT1_sgBIRC6-4A_H2LK3BGX9
4_JIMT1_sgBIRC6-4A_H2LK3BGX9


title: HCC95, sgBIRC6-4, rep 2

description:
1_HCC95_sgBIRC6-4B_H2LK3BGX9
2_HCC95_sgBIRC6-4B_H2LK3BGX9
3_HCC95_sgBIRC6-4B_H2LK3BGX9
4_HCC95_sgBIRC6-4B_H2LK3BGX9

value: lung

value: lung cance cells


title: JNKKO-BBTGF3

data_processing:
Quality Control, Alignment and Annotation were performed using COMPSRA
First, the adapters were trimmed along with any randomized bases
COMPSRA uses STAR to align clean reads to reference genome.
The aligned reads are then quantified and annotated in COMPSRA's annotation module.
Genome_build: hg38
Supplementary_files_format_and_content: tab separated files include UMI removed read count values for each Sample

extract_protocol: Acini structures  were removed from GFR- matrigel using cell recovery buffer (Thermo Fisher Cat# 50-823-93) on ice and total RNA was harvested using miRNeasy kit with DNase I treatment (QIAGEN# 217084).

treatment_protocol: For the experiment, cells were grown on growth factor reduced(GFR) matrigel within assay media ( DMEM/F12 supplemented with 2% donor horse serum and insulin,  cholera toxin, hydrocortisone,  penicillin and streptomycin). On day 7, EGF replaced with either Ethanol (control) or B/B homodimerizer in combination with or without TGF-β1 for 14 days.

value: Mammary epithelial cell line

value: JNK knockout

value: B/B homodimerizer+TGF-beta1


title: II99

tag: age

value: mucinous


title: G059_O04_CyCMV_36485_BD7_RNA_mRNAseq_run09_S6


title: HCC95, sgBIRC6-4, rep 1

description:
1_HCC95_sgBIRC6-4A_H2LK3BGX9
2_HCC95_sgBIRC6-4A_H2LK3BGX9
3_HCC95_sgBIRC6-4A_H2LK3BGX9
4_HCC95_sgBIRC6-4A_H2LK3BGX9

value: BIRC6 KO


title: G058_O04_CyCMV_36480_BD7_RNA_mRNAseq_run08_S15

value: Protected


title: II98

tag: grading


title: HCC95, sgBIRC6-1, rep 2

description:
1_HCC95_sgBIRC6-1B_H2LK3BGX9
2_HCC95_sgBIRC6-1B_H2LK3BGX9
3_HCC95_sgBIRC6-1B_H2LK3BGX9
4_HCC95_sgBIRC6-1B_H2LK3BGX9


title: JNKKO-BBTGF1


title: II90

tag: Stage

value: IIA

value: clear cells


title: II91

value: IC

tag: histotype

value: endometroid


title: JIMT1, sgCh2-2, rep 1

description:
1_JIMT1_sgCh2-2A_H2LK3BGX9
2_JIMT1_sgCh2-2A_H2LK3BGX9
3_JIMT1_sgCh2-2A_H2LK3BGX9
4_JIMT1_sgCh2-2A_H2LK3BGX9

value: breast

value: breast cancer cells


title: IH55

value: IA

tag: disease state

value: early stage ovarian cancer


title: IG70


title: G055_O04_CyCMV_36485_DX1_RNA_mRNAseq_run10_S7

value: Boost

value: F

value: Whole Blood


title: JNKKO-BB1

value: Mammary epithelial cell line

value: B/B homodimerizer

value: 21 days= 7+14day with treatments


title: G054_O04_CyCMV_36480_DX1_RNA_mRNAseq_run09_S7


title: JNKKO-BB2

value: JNK knockout


title: IJ35


title: II89


title: JNKKO-Cntrl3

value: Control


title: HCC95, sgCh2-2, rep 1

description:
1_HCC95_sgCh2-2A_H2LK3BGX9
2_HCC95_sgCh2-2A_H2LK3BGX9
3_HCC95_sgCh2-2A_H2LK3BGX9
4_HCC95_sgCh2-2A_H2LK3BGX9

value: lung

value: lung cance cells

value: control sgRNA


title: SNU503, sgBIRC6-4, rep 2

description:
1_SNU503_sgBIRC6-4B_H2LK3BGX9
2_SNU503_sgBIRC6-4B_H2LK3BGX9
3_SNU503_sgBIRC6-4B_H2LK3BGX9
4_SNU503_sgBIRC6-4B_H2LK3BGX9

value: colon

value: colorectal cancer cells

value: BIRC6 KO


title: G053_O04_CyCMV_36479_DX1_RNA_mRNAseq_run10_S3

value: Unprotected


title: IH11

value: IB

value: endometroid


title: JNKKO-BBTGF2

value: B/B homodimerizer+TGF-beta1


title: SNU503, sgBIRC6-4, rep 1

description:
1_SNU503_sgBIRC6-4A_H2LK3BGX9
2_SNU503_sgBIRC6-4A_H2LK3BGX9
3_SNU503_sgBIRC6-4A_H2LK3BGX9
4_SNU503_sgBIRC6-4A_H2LK3BGX9


title: JNKKO-Cntrl2


title: G052_O04_CyCMV_36490_BD1_RNA_mRNAseq_run10_S13

value: Boost

value: F


title: G057_O04_CyCMV_36479_BD7_RNA_mRNAseq_run11_S8

value: Whole Blood


title: BM37-PBMC2-ADT Peripheral blood mononuclear cells, ADT library, replicate 2

city: West Point

first: Ryan

last: Staupe

state: PA

address: 770 Sumneytown Pike

institute: Merck & Co., Inc.

description:
Peripheral blood mononuclear cells, ADT library, replicate 2
protein

data_processing:
Raw sequencing data were aligned to the rhesus macaque genome (Mmul_8.0.1, Ensembl v97) and counted using 10x Genomics Cell Ranger 3.1.1 (10x Genomics). Outputs from Cell Ranger were loaded into R (4.0.2) and processed using the Seurat R package (v 4.0.4).
Assembly: Mmul_8.0.1, Ensembl v97
Supplementary files format and content: 10x Genomics output files for filtered and raw data: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

organism: Macaca mulatta

source_name: Blood

extract_protocol:
Single cell suspensions were prepared from whole femur bone marrow, lymph nodes, and peripheral blood samples obtained from each rhesus macaque. Gradient density centrifugation was used to fractionate each single cell suspension and mononuclear cells were collected. Mononuclear cells were treated with ACK lysis buffer to remove red blood cells. Purified mononuclear cells were enumerated and 1*10^6 cells from each sample were stained with a panel of 124 oligo-conjugated antibodies targeting cell surface proteins or isotype controls (TotalSeqA; Biolegend). Following antibody staining, cells were loaded into a 10x Genomics Chromium Instrument. Two biological replicate samples per tissue per animal were generated targeting a cell recovery of 10,000 cells per sample.
Libraries were generated using 10x Genomics 3' scRNAseq v3.1 kit with feature barcoding per manufactuer's recommendations. ADT libraries were contructed according to manufacturer's recommendations using the TotalSeqA Reagent Kit v3 3.1 (Biolegend). Final libraries were pooled at a ratio of 80:20 RNA:ADT prior to sequencing. 100,000 reader per cell were targeted for RNA libraries and 25,000 reads per cell were targeted for ADT libraries.
OTHER: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

value: Blood

value: Mononuclear cells

value: male

tag: library type

value: ADT


title: SNU503, sgBIRC6-1, rep 2

description:
1_SNU503_sgBIRC6-1B_H2LK3BGX9
2_SNU503_sgBIRC6-1B_H2LK3BGX9
3_SNU503_sgBIRC6-1B_H2LK3BGX9
4_SNU503_sgBIRC6-1B_H2LK3BGX9


title: HCC95, sgBIRC6-1, rep 1

description:
1_HCC95_sgBIRC6-1A_H2LK3BGX9
2_HCC95_sgBIRC6-1A_H2LK3BGX9
3_HCC95_sgBIRC6-1A_H2LK3BGX9
4_HCC95_sgBIRC6-1A_H2LK3BGX9

value: lung


title: JNKKO-BB3

value: Mammary epithelial cell line

value: JNK knockout

value: B/B homodimerizer

tag: time

value: 21 days= 7+14day with treatments


title: BM37-PBMC2-GEX Peripheral blood mononuclear cells, mRNA library, replicate 2

description:
Peripheral blood mononuclear cells, mRNA library, replicate 2
polyA RNA

tag: age (years)

value: mRNA


title: HCC95, sgCh2-2, rep 2

description:
1_HCC95_sgCh2-2B_H2LK3BGX9
2_HCC95_sgCh2-2B_H2LK3BGX9
3_HCC95_sgCh2-2B_H2LK3BGX9
4_HCC95_sgCh2-2B_H2LK3BGX9

value: lung cance cells

value: control sgRNA


title: JNKKO-Cntrl1

value: Control


title: G056_O04_CyCMV_36490_DX1_RNA_mRNAseq_run11_S2

tag: group

value: Unprotected


title: BM37-PBMC1-ADT Peripheral blood mononuclear cells, ADT library, replicate 1

description:
Peripheral blood mononuclear cells, ADT library, replicate 1
protein


title: WT-BBTGF3

value: B/B homodimerizer+TGF-beta1


title: BM37-PBMC1-GEX Peripheral blood mononuclear cells, mRNA library, replicate 1

description:
Peripheral blood mononuclear cells, mRNA library, replicate 1
polyA RNA


title: G049_O04_CyCMV_36479_BD1_RNA_mRNAseq_run07_S8

value: Boost

tag: outcome

value: F


title: SNU503, sgCh2-2, rep 2

description:
1_SNU503_sgCh2-2B_H2LK3BGX9
2_SNU503_sgCh2-2B_H2LK3BGX9
3_SNU503_sgCh2-2B_H2LK3BGX9
4_SNU503_sgCh2-2B_H2LK3BGX9

value: colon

value: colorectal cancer cells


title: WT-BBTGF2

value: Wild type


title: BM37-LN2-ADT Lymph node mononuclear cells, ADT library, replicate 2

description:
Lymph node mononuclear cells, ADT library, replicate 2
protein

source_name: Lymph node

value: Lymph node

value: Mononuclear cells

value: male

value: ADT


title: G050_O04_CyCMV_36480_BD1_RNA_mRNAseq_run07_S4

value: Protected

tag: time point

value: Whole Blood


title: SNU503, sgCh2-2, rep 1

description:
1_SNU503_sgCh2-2A_H2LK3BGX9
2_SNU503_sgCh2-2A_H2LK3BGX9
3_SNU503_sgCh2-2A_H2LK3BGX9
4_SNU503_sgCh2-2A_H2LK3BGX9


title: G048_O04_CyCMV_36490_BD0_RNA_mRNAseq_run07_S5

tag: Sex


title: WT-BBTGF1

value: Mammary epithelial cell line

tag: cell line

value: 21 days= 7+14day with treatments


title: G047_O04_CyCMV_36485_BD0_RNA_mRNAseq_2_run13_S29

tag: tissue


title: BM37-LN1-ADT Lymph node mononuclear cells, ADT library, replicate 1

description:
Lymph node mononuclear cells, ADT library, replicate 1
protein

tag: cell type


title: HCC202, sgBIRC6-4, rep 1

description:
1_HCC202_sgBIRC6-4A_H2LK3BGX9
2_HCC202_sgBIRC6-4A_H2LK3BGX9
3_HCC202_sgBIRC6-4A_H2LK3BGX9
4_HCC202_sgBIRC6-4A_H2LK3BGX9

value: breast

value: breast cancer cells

tag: genotype

value: BIRC6 KO


title: WT-BB2

tag: treatment

value: B/B homodimerizer


title: WT-BB3


title: G046_O04_CyCMV_36480_BD0_RNA_mRNAseq_run11_S1

value: Boost


title: SNU503, sgBIRC6-1, rep 1

description:
1_SNU503_sgBIRC6-1A_H2LK3BGX9
2_SNU503_sgBIRC6-1A_H2LK3BGX9
3_SNU503_sgBIRC6-1A_H2LK3BGX9
4_SNU503_sgBIRC6-1A_H2LK3BGX9


title: WT-BB1


title: HCC202, sgBIRC6-1, rep 2

description:
1_HCC202_sgBIRC6-1B_H2LK3BGX9
2_HCC202_sgBIRC6-1B_H2LK3BGX9
3_HCC202_sgBIRC6-1B_H2LK3BGX9
4_HCC202_sgBIRC6-1B_H2LK3BGX9


title: BM37-LN1-GEX Lymph node mononuclear cells, mRNA library, replicate 1

description:
Lymph node mononuclear cells, mRNA library, replicate 1
polyA RNA

value: mRNA


title: BM37-BM2-ADT Bone marrow mononuclear cells, ADT library, replicate 2

description:
Bone marrow mononuclear cells, ADT library, replicate 2
protein

source_name: Bone marrow

value: Bone marrow


title: G051_O04_CyCMV_36485_BD1_RNA_mRNAseq_run11_S3

value: F


title: HCC202, sgBIRC6-1, rep 1

description:
1_HCC202_sgBIRC6-1A_H2LK3BGX9
2_HCC202_sgBIRC6-1A_H2LK3BGX9
3_HCC202_sgBIRC6-1A_H2LK3BGX9
4_HCC202_sgBIRC6-1A_H2LK3BGX9


title: G045_O04_CyCMV_36479_BD0_RNA_mRNAseq_run09_S8

value: Unprotected


title: G044_O04_CyCMV_36490_D1_RNA_mRNAseq_run12_S25

value: Prime


title: WT-Cntrl3

value: Wild type

value: Control


title: BM37-BM2-GEX Bone marrow mononuclear cells, mRNA library, replicate 2

description:
Bone marrow mononuclear cells, mRNA library, replicate 2
polyA RNA

value: Mononuclear cells

value: male


title: WT-Cntrl2


title: G043_O04_CyCMV_36485_D1_RNA_mRNAseq_run13_S19

value: Protected

value: Whole Blood


title: HCC202, sgBIRC6-4, rep 2

description:
1_HCC202_sgBIRC6-4B_H2LK3BGX9
2_HCC202_sgBIRC6-4B_H2LK3BGX9
3_HCC202_sgBIRC6-4B_H2LK3BGX9
4_HCC202_sgBIRC6-4B_H2LK3BGX9


title: WT-Cntrl1

value: Mammary epithelial cell line

value: 21 days= 7+14day with treatments


title: BM37-LN2-GEX Lymph node mononuclear cells, mRNA library, replicate 2

description:
Lymph node mononuclear cells, mRNA library, replicate 2
polyA RNA

value: Lymph node


title: HCC202, sgCh2-2, rep 1

description:
1_HCC202_sgCh2-2A_H2LK3BGX9
2_HCC202_sgCh2-2A_H2LK3BGX9
3_HCC202_sgCh2-2A_H2LK3BGX9
4_HCC202_sgCh2-2A_H2LK3BGX9

value: breast

value: breast cancer cells

value: control sgRNA


title: G042_O04_CyCMV_36480_D1_RNA_mRNAseq_run10_S5


title: BM36-PBMC2-ADT Peripheral blood mononuclear cells, ADT library, replicate 2

description:
Peripheral blood mononuclear cells, ADT library, replicate 2
protein

value: Blood

value: ADT


title: G041_O04_CyCMV_36479_D1_RNA_mRNAseq_run10_S8

value: F


title: BM37-BM1-ADT Bone marrow mononuclear cells, ADT library, replicate 1

description:
Bone marrow mononuclear cells, ADT library, replicate 1
protein

value: Bone marrow


title: CB, METplus, H3K4me3, Abcam

city: Groningen

first: JJ

last: Schuringa

address: Hanzeplein 1

department: Experimental Hematology

country: Netherlands

institute: UMCG

library_source: genomic

data_processing:
Sequenced reads were trimmed for adapter sequences.
Data analysis was done as described in Orlando et al. 2014.
In short, metagenomes were generated for human hg38 and mm10. Paired-end reads were aligned to the reference metagenome using BWA with default settings.
Generated SAM files were split into a file containing the reads aligning to human chromosomes and a file containing the reads aligning to mouse chromosomes.
Bigwig files were generated using BEDTools and BedGrapToBigWig from UCSC
Peaks were called using MACS2 with the estimated fragment size using broad settings
Assembly: hg38 and mm10
Supplementary files format and content: BigWig

molecule: genomic DNA

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes, followed by quenching and cell lysis. Next, cells were sonicated using a Bioruptor (Diagenode) and samples were spiked with mouse chromatin.
ChIP-seq libraries were generated using the KAPA Hyper Prep Kit (Roche Sequencing and Life Sciences) according to manufacturer's protocol and sequenced on an Illumina NextSeq500 using default parameters

value: CD34+ Cord Blood

value: Human hematopoietic stem and progenitors leukemia

tag: chip antibody

value: H3K4me3 (Diagenode; C15410003)

value: Plus methionine


title: CB, METplus, H3K36me3, Abcam


title: BM37-BM1-GEX Bone marrow mononuclear cells, mRNA library, replicate 1

description:
Bone marrow mononuclear cells, mRNA library, replicate 1
polyA RNA

value: Mononuclear cells

value: male

value: mRNA


title: HUPEC_15_G0G0_D3

city: Bethesda

first: Teruhiko

last: Yoshida

state: Maryland

address: 10 Center Drive, 9N208

department: NIDDK - KDB

institute: National Institutes of Health

data_processing:
Illumina RTA v3.4.4 software was used for base calling. Bcl2fastq v2.17 was used for sample demultiplexing.
Adapters from the samples were trimmed using Cutadapt 1.18 software.
Genome mapping and transcript annotation were using STAR v2.7.0f with reference genome hg38 and HIV-1 (NC_001802.1) and GENCODE v30 for human genome.
The gene expression quantification analysis was performed for all samples using RSEM 1.3.1.
Genome_build: hg38 and HIV-1: NC_001802.1
Supplementary_files_format_and_content: RawCountFile_rsemgenes.xlsx

source_name: podocyte-like epithelial cells (HUPEC)

growth_protocol: Undifferentiated podocytes were cultured in RPMI 1640 medium (Gibco, ThermoFisher Scientific, Gaithersburg, MD), supplemented with 10% fetal bovine serum and insulin/transferrin/selenium (Gibco, Thermo Fisher Scientific, Gaithersburg, MD) at 33 °C, 95% air and 5% CO2) for expansion.

extract_protocol:
Cells were resuspended with QIAzol (QIAGEN, Hilden, Germany) and RNA was extracted (Zymo Direct-zol RNA miniprep kit).
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded Total RNA library protocol.

treatment_protocol: Podocytes were differentiated by culturing in the same medium formulation at 37°C for 14 days, exchanging medium every 2-3 days.

tag: differentiation status

value: Differentiated

value: APOL1 G0/G0


title: HCC202, sgCh2-2, rep 2

description:
1_HCC202_sgCh2-2B_H2LK3BGX9
2_HCC202_sgCh2-2B_H2LK3BGX9
3_HCC202_sgCh2-2B_H2LK3BGX9
4_HCC202_sgCh2-2B_H2LK3BGX9


title: CB, METmin, H3K36me3, Abcam

value: Min methionine


title: HUPEC_13_G1G2_D3

value: APOL1 G1/G2


title: G039_O04_CyCMV_36958_D14_RNA_mRNAseq_2_run09_S13

value: Prime

value: Unprotected

value: M

value: Whole Blood


title: BM36-PBMC1-ADT Peripheral blood mononuclear cells, ADT library, replicate 1

description:
Peripheral blood mononuclear cells, ADT library, replicate 1
protein

value: Blood

value: ADT


title: HUPEC_13_G1G2_D2


title: G040_O04_CyCMV_36959_D14_RNA_mRNAseq_2_run11_S12


title: G037_O04_CyCMV_36953_D14_RNA_mRNAseq_2_run08_S16

value: Protected


title: CB, METmin, H3K4me3, Abcam

value: CD34+ Cord Blood

value: Human hematopoietic stem and progenitors leukemia


title: CB, METmin, H3K4me1, Abcam

value: H3K4me1 (Diagenode; C15410194)


title: HUPEC_15_G0G0_D1


title: HUPEC_13_G1G2_D1


title: G038_O04_CyCMV_36957_D14_RNA_mRNAseq_2_run07_S15


title: BM36-LN1-ADT Lymph node mononuclear cells, ADT library, replicate 1

value: Lymph node

value: Mononuclear cells


title: G035_O04_CyCMV_36958_D7_RNA_mRNAseq_2_run13_S20


title: G036_O04_CyCMV_36959_D7_RNA_mRNAseq_2_run13_S21


title: HL60, METplus, H3K36me3, Abcam

value: Human myeloid leukemia

value: Plus methionine


title: BM36-LN1-GEX Lymph node mononuclear cells, mRNA library, replicate 1

value: male

value: mRNA


title: BM36-PBMC1-GEX Peripheral blood mononuclear cells, mRNA library, replicate 1

description:
Peripheral blood mononuclear cells, mRNA library, replicate 1
polyA RNA


title: BM36-BM2-ADT Bone marrow mononuclear cells, ADT library, replicate 2

value: Bone marrow


title: HL60, METplus, H3K4me3, Abcam

value: H3K4me3 (Diagenode; C15410003)


title: HUPEC_12_G1G2_D2

value: Differentiated

value: APOL1 G1/G2


title: CB, METplus, H3K4me1, Abcam


title: G034_O04_CyCMV_36957_D7_RNA_mRNAseq_2_run10_S10

value: Prime

value: M

value: Whole Blood


title: BM36-PBMC2-GEX Peripheral blood mononuclear cells, mRNA library, replicate 2

description:
Peripheral blood mononuclear cells, mRNA library, replicate 2
polyA RNA

value: Blood


title: BM36-BM2-GEX Bone marrow mononuclear cells, mRNA library, replicate 2


title: HL60, METplus, H3K4me1, Abcam


title: HUPEC_12_G1G2_D1


title: HUPEC_10_G0G0_D3

value: APOL1 G0/G0


title: G032_O04_CyCMV_36959_D3_RNA_mRNAseq_2_run11_S5

value: Unprotected


title: G033_O04_CyCMV_36953_D7_RNA_2_mRNAseq_2_merged

value: Protected


title: HL60, METmin, H3K36me3, Abcam

value: Min methionine


title: BM36-BM1-ADT Bone marrow mononuclear cells, ADT library, replicate 1

value: Mononuclear cells

value: ADT


title: BM36-BM1-GEX Bone marrow mononuclear cells, mRNA library, replicate 1


title: HL60, METmin, H3K4me3, Abcam

value: Human myeloid leukemia


title: HUPEC_10_G0G0_D2


title: HUPEC_12_G1G2_D3


title: G031_O04_CyCMV_36958_D3_RNA_mRNAseq_2_run09_S14


title: BM35-PBMC2-ADT Peripheral blood mononuclear cells, ADT library, replicate 2

value: female


title: HUPEC_10_G0G0_D1


title: HL60, METmin, H3K4me1, Abcam

value: H3K4me1 (Diagenode; C15410194)


title: G030_O04_CyCMV_36957_D3_RNA_mRNAseq_2_run09_S10


title: BM35-PBMC2-GEX Peripheral blood mononuclear cells, mRNA library, replicate 2

value: mRNA


title: G029_O04_CyCMV_36953_D3_RNA_2_mRNAseq_2_run09_S2


title: BM35-PBMC1-ADT Peripheral blood mononuclear cells, ADT library, replicate 1


title: IgG-41-FGF

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

institute: Radboud University

data_processing:
initial quality check with FastQC
Sequencing reads were aligned using STAR 2.5.0 with default options.
For data visualization, wigToBigWig from the UCSC genome browser tools was used to generate bigwig files and uploaded to UCSC genome browser.
Assembly: human genome assembly hg19
Supplementary files format and content: bigwig file

source_name: skin samples

growth_protocol: Dermal fibroblasts (donor 38 and 41) were cultured in high glucose-DMEM containing 10% EV-depleted FCS, L-glutamine and 1% penicillin/streptomycin in 6-well plates.

extract_protocol:
RNA was extracted using RNEasy Mini kit with gDNA eliminators columns (QIAGEN). RNA-Seq experiment was performed with the starting material of 500 ng total RNA.
The prepared libraries were quantified with the KAPA Library Quantification Kit (KK4844, KAPA Biosystems, Roche), and then sequenced in a paired-ended manner using the NextSeq 500 (Illumina) according to standard Illumina protocols.

treatment_protocol: Cells were treated with CTL-EV , FGF2-EVs (2E+10p) or FGF2 (100 ng/ml). Some samples were pre-treated with neutralizing FGF2 antibody or IgG control (1 ug/ml) 1h before EV treatment. Cells were washed  with PBS 24h later and trypsinized for collection.

value: skin samples

value: Primary human dermal fibroblasts (DF)

tag: donor

value: donor 41

value: FGF-treated cells with igG antibody


title: G028_O04_CyCMV_36959_D0_RNA_mRNAseq_2_run10_S2

value: Prime

value: M


title: IgG-41-EFGF

value: FGF exosome treated cells with igG antibody


title: HUPEC_15_G0G0_UD2

value: Undifferentiated

value: APOL1 G0/G0


title: HUPEC_15_G0G0_UD3


title: IgG-41-ECTRL

value: control exosome treated cells with igG antibody


title: HUPEC_15_G0G0_UD1


title: G027_O04_CyCMV_36958_D0_RNA_mRNAseq_2_run12_S24

value: Unprotected

value: Whole Blood


title: IgG-41-CTRL

value: untreated cells with igG antibody


title: BM35-LN2-ADT Lymph node mononuclear cells, ADT library, replicate 2

description:
Lymph node mononuclear cells, ADT library, replicate 2
protein

value: Lymph node

value: Mononuclear cells

value: ADT


title: HUPEC_13_G1G2_UD3

value: APOL1 G1/G2


title: G026_O04_CyCMV_36957_D0_RNA_mRNAseq_2_run11_S9

value: Protected


title: HUPEC_13_G1G2_UD2


title: IgG-38-FGF

value: skin samples

value: Primary human dermal fibroblasts (DF)

value: donor 38


title: G025_O04_CyCMV_36953_D0_RNA_2_mRNAseq_2_run12_S19

value: Prime


title: BM35-LN1-ADT Lymph node mononuclear cells, ADT library, replicate 1

description:
Lymph node mononuclear cells, ADT library, replicate 1
protein

value: female


title: IgG-38-EFGF

value: FGF exosome treated cells with igG antibody


title: HUPEC_13_G1G2_UD1

value: Undifferentiated


title: G024_O04_CyCMV_36490_D14_RNA_2_mRNAseq_2_run10_S4

value: F


title: BM35-LN1-GEX Lymph node mononuclear cells, mRNA library, replicate 1

value: mRNA


title: HUPEC_12_G1G2_UD3


title: IgG-38-ECTRL

value: control exosome treated cells with igG antibody


title: G023_O04_CyCMV_36485_D14_RNA_mRNAseq_2_run10_S14

value: Whole Blood


title: BM35-BM2-ADT Bone marrow mononuclear cells, ADT library, replicate 2

value: Bone marrow


title: IgG-38-CTRL

value: untreated cells with igG antibody


title: BM35-PBMC1-GEX Peripheral blood mononuclear cells, mRNA library, replicate 1

value: Blood

value: Mononuclear cells


title: HUPEC_12_G1G2_UD2

value: APOL1 G1/G2


title: G022_O04_CyCMV_36480_D14_RNA_2_mRNAseq_2_run11_S13

value: Protected


title: aFGF-41-FGF

value: skin samples

value: donor 41

value: FGF-treated cells with FGF antibody


title: G021_O04_CyCMV_36479_D14_RNA_mRNAseq_2_merged

value: Prime

value: Unprotected


title: aFGF-41-EFGF

value: Primary human dermal fibroblasts (DF)

value: FGF exosome treated cells with FGF antibody


title: HUPEC_10_G0G0_UD3

value: Undifferentiated

value: APOL1 G0/G0


title: BM35-BM1-ADT Bone marrow mononuclear cells, ADT library, replicate 1

value: female

value: ADT


title: BM35-BM2-GEX Bone marrow mononuclear cells, mRNA library, replicate 2

value: Bone marrow

value: mRNA


title: G018_O04_CyCMV_36490_D7_RNA_mRNAseq_2_run07_S14

value: F

value: Whole Blood


title: aFGF-41-ECTRL

value: control exosome treated cells with FGF antibody


title: BM35-BM1-GEX Bone marrow mononuclear cells, mRNA library, replicate 1

value: Mononuclear cells


title: BM35-LN2-GEX Lymph node mononuclear cells, mRNA library, replicate 2

value: Lymph node


title: HUPEC_10_G0G0_UD2


title: aFGF-41-CTRL

value: skin samples

value: donor 41

value: untreated cells with FGF antibody


title: BM23-PBMC2-ADT Peripheral blood mononuclear cells, ADT library, replicate 2

value: Blood

value: male


title: G016_O04_CyCMV_36480_D7_RNA_mRNAseq_2_run07_S1

value: Prime

value: Protected


title: aFGF-38-FGF

value: Primary human dermal fibroblasts (DF)

value: donor 38

value: FGF-treated cells with FGF antibody


title: HUPEC_10_G0G0_UD1

value: Undifferentiated

value: APOL1 G0/G0


title: MGE organoid from individual L7

city: New York City

first: Jaroslav

last: Bendl

state: New York

address: One Gustave L. Levy Place, Department of Genetics and Genomics Sciences, Box 1210

department: Genetics and Genomics Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing paired-end files were aligned by STAR (v2.7.0.e) (Dobin et al. 2013) to the hg38 reference genome with the pseudoautosomal region masked on chromosome Y using the following parameters: --alignIntronMax 1 --out FilterMismatchNmax 100 --alignEndsType EndToEnd --out FilterScoreMinOverLread 0.3 --out FilterMatchNminOverLread 0.3. This yielded for each sample a BAM file of mapped paired-end reads sorted by genomic coordinates. From these BAM-files, we removed reads that were mapped to multiple loci or to the mitochondrial genome using samtools (v0.1.19) (Li et al. 2009) as well as the duplicated reads using PICARD (v2.24; http://broadinstitute.github.io/picard). The read coverage files (bedGraph) were generated by genomeCoverageBed from BEDTools (v2.25.0) (Quinlan and Hall 2010) and converted to the indexed binary format files (bigWig) using bedGraphToBigWig.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: MGE organoid

growth_protocol: iPSCs were differentiated into cortical organoid mostly comprised with glutamatergic neurons vs MGE organoid mostly comprised with cortical interneurons according to an established protocol (PMID: 33097921).

extract_protocol:
50mg of frozen brain tissue was homogenized in cold lysis buffer (0.32M Sucrose, 5 mM CaCl2, 3 mM Mg(Ace)2, 0.1 mM, EDTA, 10mM Tris-HCl, pH8, 1 mM DTT, 0.1% Triton X-100) and filtered through a 40µm cell strainer. The flow-through was underlaid with sucrose solution (1.8 M Sucrose, 3 mM Mg(Ace)2, 1 mM DTT, 10 mM Tris-HCl, pH8) and subjected to ultracentrifugation at 24,000 rpm for 1 hour at 4°C. Pellets were thoroughly resuspended in 500µl DPBS and incubated in BSA (final concentration 0.1%) and anti-NeuN antibody (1:1000, Alexa488 conjugated, Millipore) under rotation for 1 hour, at 4 °C, in the dark. Prior to FANS sorting, DAPI (Thermoscientific) was added to a final concentration of 1µg/ml. DAPI positive neuronal (NeuN+) and non-neuronal (NeuN-) nuclei were sorted into tubes pre-coated with 5%BSA using a BD-FACSAria flow cytometer (BD Biosciences) equipped with a 70μm nozzle.
ATAC-seq reactions were performed using an established protocol (PMID25559105) with minor modifications. Media was removed and replaced with 200 µl of 1X Trypsin and 100mM trehalose. Tubes were incubated at 37°C for 10 minutes, after which dissociation was performed by gentle pipetting. Trypsin was neutralized by the addition of 200µl DMEM +10% FBS containing 0.5 µl turbo DNase and samples incubated for an additional 20 min at 37°C. Cells were then centrifuged at 300 g for 10 min at 4°C and pellets resuspended in 250µl PBS + 5% BSA. DAPI (Thermofisher) was added to the cells and viable (DAPI-) cells sorted on a FACSAria flow cytometer (BD Biosciences). Following FACS, cell concentrations and viability were confirmed using a Countess automated cell counter (Life technologies) and, where available, 75,000 cells were carried forward for the ATAC-seq reactions. Cells were centrifuged at 300 g for 10 min at 4°C and, following removal of the supernatant, pellets were resuspended in lysis buffer (10mM Tris-Cl pH7.4, 10mM NaCl, 3mM MgCl, 0.1% IGEPAL CA630) by pipetting 20 times. Following resuspension, samples were centrifuged at 500 g
 for 10 min at 4°C. Pellets were resuspended in transposase reaction mix (25 μL 2x TD Buffer (Illumina Cat #FC-121-1030) 2.5 μL Tn5 Transposase (Illumina Cat #FC-121-1030) and 22.5 μL Nuclease Free H2O) on ice. Reactions were incubated at 37°C for 30 min before being purified using the MinElute Reaction Cleanup kit (Qiagen Cat #28204). Following purification, library fragments were amplified using the Nextera index kit (Illumina Cat #FC-121-1011) as previously described (PMID25559105). Library quality was assessed on a Tapestation instrument using D5000 ScreenTapes (Agilent technologies Cat# 5067-5588). Following amplification, libraries were resolved on 2% agarose gels and fragments ranging in size from 100-1000bp were excised and purified (Qiagen Minelute Gel Extraction Kit – Qiagen Cat#28604). Before sequencing, library fragment sizes estimated using Tapestation D5000 ScreenTapes (Agilent technologies Cat# 5067-5588) and libraries quantified by quantitative PCR (KAPA Biosystems Cat#KK4873) and). Finally, libraries were sequenced on the NovaSeq6000 platform (Illumina) obtaining 2x100 paired-end reads.

tag: person id

value: MGE organoid

tag: gender

value: Male

tag: ethnicity

value: Caucasian

tag: diagnosis

value: Control


title: G015_O04_CyCMV_36479_D7_RNA_mRNAseq_2_run09_S5

tag: age (years)

value: Unprotected

value: F

value: Whole Blood


title: MGE organoid from individual L9


title: BM23-PBMC1-ADT Peripheral blood mononuclear cells, ADT library, replicate 1

value: Mononuclear cells

tag: library type

value: ADT


title: aFGF-38-EFGF

value: skin samples

value: FGF exosome treated cells with FGF antibody


title: BM23-PBMC2-GEX Peripheral blood mononuclear cells, mRNA library, replicate 2

value: Blood

value: male

value: mRNA


title: HUPEC_12_G1G2_UD1

value: APOL1 G1/G2


title: G012_O04_CyCMV_36490_D3_RNA_mRNAseq_2_run09_S11

tag: group

value: Prime

tag: outcome


title: G011_O04_CyCMV_36485_D3_RNA_2_mRNAseq_2_run12_S27

value: Protected

tag: time point

tag: Sex


title: BM23-PBMC1-GEX Peripheral blood mononuclear cells, mRNA library, replicate 1

tag: tissue


title: aFGF-38-CTRL

tag: cell type

value: Primary human dermal fibroblasts (DF)

value: donor 38

value: untreated cells with FGF antibody


title: MGE organoid from individual 483

value: MGE organoid

value: Male

value: Caucasian

value: Control


title: G010_O04_CyCMV_36480_D3_RNA_2_mRNAseq_2_run07_S13

value: F

value: Whole Blood


title: aFGF-38-ECTRL

value: skin samples

value: control exosome treated cells with FGF antibody


title: BM23-LN2-ADT Lymph node mononuclear cells, ADT library, replicate 2

value: Lymph node

value: Mononuclear cells

value: ADT


title: MGE organoid from individual 689


title: BM23-LN2-GEX Lymph node mononuclear cells, mRNA library, replicate 2

value: male

value: mRNA


title: COVID PASC hyposmic patient 6

city: Durham

first: John

last: Finlay

state: NC

address: 40 Duke Medicine Circle

institute: Duke University

description: COVID 6

library_source: transcriptomic single cell

data_processing:
Raw base call files were analyzed using Cell Ranger v.4.0.0 using the Duke Cluster Computing platform. The ‘mkfastq’ command was used to generate FASTQ files from bcl Illumina sequencer output files.
CellRanger v.4.0.0 ‘counts’ command was used to generate raw gene-barcode matrices aligned to the GRCh38-2020-A Ensembl 98 human genome
Assembly: GRCh38-2020-A Ensembl 98
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mx

source_name: adult human olfactory epithelium

extract_protocol:
Biopsy specimens were collected in either HBSS + 10% FBS or Hibernate E Media +10% FBS, spun down, then digested using collagenase I, dispase and DNAse, papain, and trypsin. Cells were filtered through a 70 μm strainer, pelleted and washed, and then treated with an erythrocyte lysis buffer and washed again. The cells were then resuspended in PBS with 0.1% bovine serum albumin and 0.2% anti-clumping agent (Invitrogen) and immediately processed for scRNA-seq. Note that COVID PASC hyposmic patient 2 was split up into two different samples prior to loading on Chromium for single cell preparation (hence COVID_2_1 and COVID_2_2 notation)
Samples were processed for scRNA-seq using Chromium Single Cell 3′ Paired-End, Dual-Index Library & Gel Bead Kit v3.1 (10X Genomics) targeting 10000 cells, then sequenced using NextSeq 150bp (Illumina) flow cells.

tag: age

tag: months post covid infection

tag: biopsy type

value: Brush


title: G017_O04_CyCMV_36485_D7_RNA_mRNAseq_2_run11_S11

value: Prime

value: Protected


title: MGE organoid from individual 190


title: BM23-LN1-ADT Lymph node mononuclear cells, ADT library, replicate 1


title: COVID PASC hyposmic patient 5

description: COVID 5


title: Cortical organoid from individual 483

source_name: Cortical organoid

value: Cortical organoid


title: G006_O04_CyCMV_36490_D0_RNA_2_mRNAseq_2_run10_S9

value: Unprotected


title: Cortical organoid from individual 190

value: Male


title: COVID PASC hyposmic patient 4

description: COVID 4


title: BM23-LN1-GEX Lymph node mononuclear cells, mRNA library, replicate 1


title: G005_O04_CyCMV_36485_D0_RNA_2_mRNAseq_2_run13_S23


title: BM23-BM2-ADT Bone marrow mononuclear cells, ADT library, replicate 2

value: Bone marrow


title: COVID PASC hyposmic patient 3

description: COVID 3

value: Surgical


title: G004_O04_CyCMV_36480_D0_RNA_2_mRNAseq_2_run12_S22

value: F


title: HS1 Hi-C rep 2

city: San Francisco

first: Katherine

middle: S

last: Pollard

state: CA

address: 1650 Owens St

department: Institute of Data Science and Biotechnology

institute: Gladstone Institutes

data_processing:
Adapters were trimmed from raw FASTQ files using TrimGalore [v0.6.5] with options --illumina --paired.
The data were then processed from adapter-trimmed FASTQ files to Hi-C contacts as cooler files using Distiller [v0.3.3] (65). This processing includes read mapping with BWA-MEM (66), filtering (MAPQ >= 30), contact pair processing with pairtools (67) and normalization via matrix balancing (68). Samples were processed both per replicate, per individual and per species. For easier comparison of samples in some analyses, we mapped the data from each species to the reference genome of the other species (human to pantro6 and chimp to hg38).
Genome_build: hg38, panTro6
Supplementary_files_format_and_content: Cooler (Hi-C contact matrices)

growth_protocol: Two human (WTC11 and HS1) and two chimpanzee (C3649 and Pt2a) induced pluripotent cell lines (iPSCs) were cultured in Matrigel-coated plates with mTeSR media (WTC11 and C3649 were cultured in StemFlex) in an undifferentiated state. Cells were propagated at a 1:3 ratio by treatment with 200 U/mL collagenase IV (or PBS-EDTA) and mechanical dissection.   WTC11 and C3649 iPSCs were differentiated to neural progenitor cells (NPCs) as previously described (64). Briefly, 2-2.5×10⁵ cells per cm² were seeded on Matrigel-coated wells in StemFlex containing 2 μM Thiazovivin. The following day (Day 0), medium was replaced with E6 containing 500 nM LDN193189 (Selleckchem), 10 μM SB431542 (Selleckchem), and 5 μM XAV-939 (Selleckchem). Starting on Day 3, medium was replaced with E6 containing 500 nM LDN193189 and 10 μM SB431542 every 48 hrs. Starting on Day 12, medium was replaced with Neurobasal containing 2 mM GlutaMAX, 60 μg per ml L-Ascorbic acid 2-phosphate, N2, and B27 without Vitamin A every 48 hours. Around Day 16, cells were washed with PBS, dissociated with Accutase, pelleted and resuspended in Neurobasal containing 2 mM GlutaMAX, 60 μg per ml L-Ascorbic acid 2-phosphate, N2, and B27 without Vitamin A, 10 ng per ml fibroblast growth factor 2, and 10 ng per ml epidermal growth factor, and seeded on poly-L-ornithine-, fibronectin-, and laminin-coated wells. Cells were collected for HiC at passage 5-7.  To differentiate HS1 and Pt2a iPSCs into NPCs, cells were split with EDTA at 1:5 ratios in culture dishes coated with matrigel and culture in N2B27 medium (comprised of DMEM/F12 medium (Invitrogen) supplemented with 1% MEM-nonessential amino acids (Invitrogen), 1 mM L-glutamine, 1% penicillin-streptomycin, 50 ng/mL bFGF (FGF-2) (Millipore), 1x N2 supplement, and 1 x B27 supplement without Vitamin A (Invitrogen)) supplemented with 100 ng/ml mouse recombinant Noggin (R&D systems). Cells at passages 1-3 were split by collagenase into small clumps, and continuously cultured in N2B27 medium with Noggin. After passage 3, cells were plated at the density of 5×10⁵ cells/cm² after disassociation by TrypLE express (Invitrogen) into single-cell suspension, and cultured in N2B27 medium supplemented with 20 ng/mL bFGF and EGF. Cells were maintained and collected at passage 18-20. Our use of two differentiation protocols reflects rapid progress in stem cell research during the course of this study.

treatment_protocol: Hi-C was performed using the Arima Hi-C kit (Arima Genomics) according to the manufacturer’s instructions. 10 million cells were used. The sequencing library was prepared using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) according to the manufacturer's protocol. Two independent biological replicates were prepared for each cell line. In total eight libraries were pooled and sequenced with paired-end 150-bp reads using two lanes of a NovaSeq6000 S2 (Illumina) at the Chan Zuckerberg Biohub.

tag: cell line

value: iPS-derived neural progenitor cells


title: BM23-BM2-GEX Bone marrow mononuclear cells, mRNA library, replicate 2


title: HS1 Hi-C rep 1

extract_protocol: The sequencing library was prepared using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) according to the manufacturer's protocol. Two independent biological replicates were prepared for each cell line. In total eight libraries were pooled and sequenced with paired-end 150-bp reads using two lanes of a NovaSeq6000 S2 (Illumina) at the Chan Zuckerberg Biohub.


title: G003_O04_CyCMV_36479_D0_RNA_mRNAseq_2_run09_S3

value: Whole Blood


title: BM23-BM1-ADT Bone marrow mononuclear cells, ADT library, replicate 1


title: G009_O04_CyCMV_36479_D3_RNA_mRNAseq_2_merged


title: COVID PASC hyposmic patient 1

description: COVID 1


title: WTC11 Hi-C rep 2


title: WTC11 Hi-C rep 1


title: BM23-BM1-GEX Bone marrow mononuclear cells, mRNA library, replicate 1


title: BM22-PBMC2-ADT Peripheral blood mononuclear cells, ADT library, replicate 2

value: Blood

value: female


title: COVID PASC hyposmic patient 2, portion 1

description: COVID 2 (sample 1)


title: TGF.SM31.rep3

city: Orléans

first: Patrick

last: Baril

address: Rue Charles Sadron

country: France

institute: Centre de Biophysique Moléculaire, CNRS-UPR4301

data_processing:
Image analysis, base calling and demultiplexing were performed using RTA 2.4.6 and bcl2fastq 2.18.12
Adapter sequences were trimmed with Cutadapt-1.15, only reads longer than 10 bp were kept for analysis
Sequences were aligned to the Human genome  with TopHat2 2.1.1 using default parameters
Uniquely mapped reads were assigned to genes with FeatureCounts- subread v.1.5.2
Differential expression analysis was performed with DESeq2,
Genome_build: Hg 19 gencode v.17
Supplementary_files_format_and_content: Matrix table with normalized abundance measurements for every gene and every sample (output from DESeq2)

molecule: polyA RNA

source_name: Spontaneously immortalized human keratinocyte cell line

extract_protocol:
Total RNA was isolated from HaCaT cells using mirVanaTM miRNA isolation kit (Ambion, Life Technologies, Cat #AM1560)
Libraries were constructed using the Illumina mRNA Stranded Kit, according to the manufacturer recommandations

value: HaCaT cells

tag: treatment


title: TGF.SM31.rep2


title: 4012_72HPI_2

city: Stockholm

first: Carl

middle: M

last: Sellgren

address: Solnavagen 1

country: Sweden

institute: Karolinska Institute

data_processing:
The Cellranger (version 5.0, 10X Genomics) pipeline was used to process input FASTQ  files for each sample obtained for single cell RNA-seq.
cellranger count pipeline was run to perform read alignment to a custom reference of combined human (GRCh38) and SARS-CoV-2 genome, UMI counting and secondary analysis (dimensional reduction, clustering,etc), for each sample separately
cellranger processed output files were read into R using the Read10X function from the Seurat package. Low-quality cells and doublets were filtered out and the data was further normalized using SCTNormalize function from Seurat.
Genome_build: GRCh38 + SARS-CoV-2 (GenBank: MT093571)
Supplementary_files_format_and_content: .loom format files of filtered read count matrices of individual 6 samples obtained as an output of cellranger. Final count matrix and metadata of all cells included in the downstream data analysis to make conclusions provided in the study.

source_name: Cerebral organoid_72HPI

growth_protocol: Briefly, embryoid bodies (EBs) were generated by seeding 9000 single cells in each well of a low attachment 96-well U-bottom plate with Y-27632 ROCK inhibitor (10 μM) for one day. EB media was replaced on day 5 with Neural induction media in the same 96-well plate. On day 10-11, EBs were embedded in 30μl Matrigel (Corning) using sheets of dimpled parafilm and incubated for 20min at 37°C as previously detailed. Matrigel embedded single EBs were then either transferred to a 24-well plate in 3ml of expansion media per well, on an orbital shaker (90 rpm), or to a 12-well miniaturized bioreactor (largely overlapping with the design proposed by Qian et al.),11 until further use.

extract_protocol:
Single cell suspensions were loaded onto a Chromium controller chip v3.1 (10X Genomics), with a target output of 6000-7000 cells per channel. GEM generation, barcoding, cDNA amplification and library preparation was performed using the Single-cell 3’ Gel Bead and Library v3.1 kit (10X Genomics) at the Eukaryotic Single Cell Genomics facility (SciLifeLab, Sweden). Amplified cDNA and final libraries were evaluated on a Bioanalyzer for quality control and sequenced on Illumina NovaSeq 6000 platform.
Single cell suspensions isolated from 3 organoids were pooled for each sample and loaded onto GEM wells. Each condition had 2 samples which were loaded onto individual GEM wells. Total number of GEM wells used were 6 (2 per experimental condition)

treatment_protocol: From single cell dissociation experiments, approximately 1×10^6 cells were found to be present in a D65 organoid. Based on this, 3×10^5 PFU/ml of SARS-CoV2 was used to infect organoids for 2h (MOI 0.3) in a spinning bioreactor. Following viral exposure, the organoids were washed twice with PBS and transferred into fresh medium (2ml) to follow the course of infection.

tag: condition

value: Healthy

value: Live SARS-CoV-2

tag: tissue/cell type

value: Cerebral organoid


title: TGF.SM31.rep1


title: BM22-PBMC1-ADT Peripheral blood mononuclear cells, ADT library, replicate 1

value: Mononuclear cells

value: ADT


title: 4011_72HPI_1


title: BM22-PBMC2-GEX Peripheral blood mononuclear cells, mRNA library, replicate 2

value: mRNA


title: 4010_24HPI_2

source_name: Cerebral organoid_24HPI


title: COVID PASC hyposmic patient 2, portion 2

description: COVID 2 (sample 2)


title: 4009_24HPI_1


title: TGF.rep3

value: TGF-β1 (10ng/ml)


title: TGF.rep2


title: BM22-LN2-ADT Lymph node mononuclear cells, ADT library, replicate 2

value: Lymph node


title: 4008_Control_uninfected_2

source_name: Cerebral organoid_control

value: Mock


title: BM22-PBMC1-GEX Peripheral blood mononuclear cells, mRNA library, replicate 1


title: CD19 opn [EN59]

first: claudia

last: Chiodoni

state: Italy

address: Via Amadeo 42

department: Department of experimental oncology

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl following the manufacturer's instructions.  25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray  for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control software

data_processing: The scanned images were analyzed with Feature Extraction Software ì (Agilent Technologies, Santa Clara, CA) using default parameters. Raw data were imported in R software through read.maimages function from limma packages with green.only parameter set to true to read the green (Cy3) channel only.

organism: Mus musculus

source_name: splenic CD19 from a OPN-/- mouse

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions

growth_protocol: CD19+ cells from the spleen were purified without in vitro culturing

extract_protocol: Total RNA was extracted using the Quick RNA micro prep kit (Zymo Research).

treatment_protocol: No treatment was performed

tag: strain/genotype

value: OPN-/- mouse

value: spleen


title: CD19 opn [EN58]


title: BM22-LN2-GEX Lymph node mononuclear cells, mRNA library, replicate 2


title: TGF.rep1


title: BM22-LN1-ADT Lymph node mononuclear cells, ADT library, replicate 1


title: 4007_Control_uninfected_1


title: TCR repertoire of P5 [P5-TCR]

city: Hidaka-City, Saitama

first: Satoshi

last: Yamasaki

department: Department of Respiratory Medicine

country: Japan

institute: Saitama Medical University

description:
P5-TCR
RNA of TCR genes
Peripheral Blood Mononuclear Cells

data_processing:
Library strategy: TCR repertoire
10x Genomics cellranger (4.0.0) mkfastq used for basecalling.
Sequenced reads were processed with cellranger (4.0.0) count using the GRCh38 reference dataset (version 2020-A; downloaded from 10x Genomics) to derive gene expression and feature barcode UMI count matrix.
Sequenced reads were processed with cellranger (4.0.0) vdj using the GRCh38 reference dataset (version 4.0.0; downloaded from 10x Genomics) to derive TCR clonotype data.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_matrix.mtx.gz: MatrixMarket format files include UMI count matrixes of gene expressions and feature barcodes for each sample. Row and column names of matrix are separately recorded in following two files.
Supplementary_files_format_and_content: *_barcodes.tsv.gz: Tab-separated text files include cell barcodes for each sample.
Supplementary_files_format_and_content: *_features.tsv.gz: Tab-separated text files include gene names and feature barcode names for each sample.
Supplementary_files_format_and_content: *_filtered_contig_annotations.csv.gz: Comma-separated text files include TCR clonotype data for each sample.

source_name: CD4+ T cells

extract_protocol:
Manufactured protocol of Chromium system (10x Genomics).
Manufactured protocol of Chromium Next GEM Single Cell V(D)J Reagent Kit v1.1 with Feature Barcoding technology (10x Genomics).

treatment_protocol: Pre-treatment samples.

tag: diagnosis

value: Lung cancer

value: CD4+ T cells


title: BM22-LN1-GEX Lymph node mononuclear cells, mRNA library, replicate 1

description:
Lymph node mononuclear cells, mRNA library, replicate 1
polyA RNA

tag: age (years)


title: HUPEC_15_G0G0_D2

tag: differentiation status

value: Differentiated

tag: genotype

value: APOL1 G0/G0


title: scRNAseq of P5 [P5-GEX]

description:
P5-GEX, P5-FB
total RNA, DNA attached to feature barcode antibody
Peripheral Blood Mononuclear Cells

data_processing:
10x Genomics cellranger (4.0.0) mkfastq used for basecalling.
Sequenced reads were processed with cellranger (4.0.0) count using the GRCh38 reference dataset (version 2020-A; downloaded from 10x Genomics) to derive gene expression and feature barcode UMI count matrix.
Sequenced reads were processed with cellranger (4.0.0) vdj using the GRCh38 reference dataset (version 4.0.0; downloaded from 10x Genomics) to derive TCR clonotype data.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_matrix.mtx.gz: MatrixMarket format files include UMI count matrixes of gene expressions and feature barcodes for each sample. Row and column names of matrix are separately recorded in following two files.
Supplementary_files_format_and_content: *_barcodes.tsv.gz: Tab-separated text files include cell barcodes for each sample.
Supplementary_files_format_and_content: *_features.tsv.gz: Tab-separated text files include gene names and feature barcode names for each sample.
Supplementary_files_format_and_content: *_filtered_contig_annotations.csv.gz: Comma-separated text files include TCR clonotype data for each sample.


title: BM22-BM2-ADT Bone marrow mononuclear cells, ADT library, replicate 2

description:
Bone marrow mononuclear cells, ADT library, replicate 2
protein

value: Bone marrow

value: female

tag: library type


title: TCR repertoire of P2 [P2-TCR]

description:
P2-TCR
RNA of TCR genes
Peripheral Blood Mononuclear Cells


title: BM22-BM2-GEX Bone marrow mononuclear cells, mRNA library, replicate 2

description:
Bone marrow mononuclear cells, mRNA library, replicate 2
polyA RNA


title: scRNAseq of P2 [P2-GEX]

description:
P2-GEX, P2-FB
total RNA, DNA attached to feature barcode antibody
Peripheral Blood Mononuclear Cells


title: BM22-BM1-ADT Bone marrow mononuclear cells, ADT library, replicate 1


title: CD19 opn [EN60]


title: CD19 b/c [EN54]

source_name: splenic CD19 from a BALB/c mouse

value: BALB/c mouse


title: TCR repertoire of P1 [P1-TCR]

description:
P1-TCR
RNA of TCR genes
Peripheral Blood Mononuclear Cells


title: CD19 b/c [ER97]


title: CD19 b/c [EN53]


title: CD19 opnlpr [EN70]

source_name: splenic CD19 from a OPN-/-Faslpr/lpr mouse with initial lymphoma


title: CD19 b/c [EN52]


title: mock expressing HT-29 cells 3

city: Seoul

first: Sujin

last: Kang

address: 50, Yonsei-ro, Seodaemun-gu

department: Department of Systems Biology

country: South Korea

institute: Yonsei University

description:
Microarray of mock expressing HT-29 cells 3
210810

hyb_protocol: Approximately 5.5mg of labeled DNA target was hybridized to the Affymetrix GeneChip Array 45℃ for 16hours

scan_protocol: CGS 3000 scanner

data_processing:
The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).
RMA analysis

label: biotin

source_name: mock expressing HT-29 cells

label_protocol: biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: HT-29 cells were cultured in 10%FBS containing RPMI media

extract_protocol: RNA were extrated with trizol methods

value: colon cancer cells

value: control


title: CD19 opn [EN57]


title: CD19 opnlpr [EN69]

value: OPN-/-Faslpr/lpr mouse with initial lymphoma


title: BM22-BM1-GEX Bone marrow mononuclear cells, mRNA library, replicate 1

value: Mononuclear cells


title: TRIM40 expressing HT-29 cells 3

description:
Microarray of TRIM40 expressing HT-29 cells 3
210810

source_name: TRIM40 expressing HT-29 cells

value: TRIM40 overexpression


title: CD19 opnlpr [EN67]


title: scRNAseq of P1 [P1-GEX]

description:
P1-GEX, P1-FB
total RNA, DNA attached to feature barcode antibody
Peripheral Blood Mononuclear Cells


title: mock expressing HT-29 cells 2

description:
Microarray of mock expressing HT-29 cells 2
210728


title: CD19 lpr [EN65]

source_name: splenic CD19 from a Faslpr/lpr mouse without lymphoma

value: Faslpr/lpr mouse without lymphoma


title: mock expressing HT-29 cells 1

description:
Microarray of mock expressing HT-29 cells 1
190530


title: CD19 lpr [EN64]


title: T cells, 15min, PBS, 1

status: Public on Dec 20 2022

type: protein

city: Freiburg

first: Natalie

last: Koehler

address: Breisacher Str. 115

country: Germany

institute: University Medical Center Freiburg

description: Protein lysates with still active kinases, phosphorylation of spotted peptides on chip detected with FITC labeled anti-phospho antibody

hyb_protocol: 5 μg of protein per well was loaded onto the PamChip and the assay was run on a PamStation96 (PamGene International).

scan_protocol: The degree of phosphorylation was measured in real time via the kinetic image capture program, Evolve (PamGene International), which captures FITC-labeled anti-phosphotyrosine antibody binding to each phosphorylated peptide substrate. Following 60 min incubation, the signal intensities for each peptide were analyzed using BioNavigator Software (PamGene International).

data_processing: Only peptides that showed kinetics (increase of signal in time) on at least 25 % of the arrays were included in the analysis. Nominal coefficient of variation (CV) was calculated per peptide using a 2-component error fit model using overall mean as input and was used as a filter to remove low-intensity spots. Only peptides that showed nominal CV <0.5 were included in the analysis. For kinase interpretation, a ranked list of putative kinases responsible for differences in the peptide phosphorylation was generated by upstream kinase analysis (UKA, PamGene International).

label: PY20 FITC

molecule: protein

source_name: T cells, PBS, 15 min stim

label_protocol: We used the PTK PamGene Array according to instructions

growth_protocol: PBMCs of healthy donors were isolated with a Ficoll. T cells were isolated using the Pan T cell isolation kit (Miltenyi). 1Mio CD4/CD8 T cells were cultured in 6-well format in 1ml RPMI+10%FCS per well.

extract_protocol: PamGene lysates were prepared according to manufacturers instructions with M-PER Mammalian Protein Extraction Reagent (ThermoFisher) containing Halt phosphatase and Halt protease inhibitor cocktails (ThermoFisher). Total protein was quantified using the Pierce BCA Protein Assay Kit (ThermoFisher).

treatment_protocol: PBS or hBD-2 (60µL/mL) were added for 20 min before T cells were stimulated with anti-CD3/anti-CD28 microbeads in a 1:1 bead-to-cell ratio for 15 min.

tag: individual

value: donor 1

tag: disease state

value: healthy

value: blood

value: PBMC

tag: cell subset

value: CD4/CD8 T cells

value: PBS

tag: pamchip number


title: CD19 lpr [EN63]

tag: Sex

tag: tissue

value: spleen


title: T cells, 15min, PBS, 3

value: donor 3

tag: cell type


title: T cells, 15min, hBD2, 1

source_name: T cells, hBD-2, 15 min stim


title: T cells, 15min, hBD2, 2

value: donor 2


title: TRIM40 expressing HT-29 cells 1

description:
Microarray of TRIM40 expressing HT-29 cells 1
190530

tag: cell line


title: SSEA4+P-S3

city: Yangling

first: Pengfei

last: Zhang

state: Shaanxi,

address: 22# Xinong Road

department: College of Animal Science and Technology

country: China

institute: Northwest A&F University

data_processing:
RNA-seq: After raw data process, high quality clean reads were aligned to the reference genome (susScr3) with hisat2 software (v2.0.4). Then, cuffdiff software (part of cufflinks) was used to get the gene level FPKM based on the Ensembl gtf gene annotation file. The differentially expressed mRNA were identified and used for further analysis.
Genome_build: Sscrofa11.1

organism: Sus scrofa

source_name: germ cells

extract_protocol:
Fractions with high purity of SSEA4-positive spermatogonia were resuspended with Trizol (Invitrogen, USA) and total RNA was extracted for further analysis.
RNA seq:total RNA was used for removing rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer’s instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumine Hiseq instrument with 150bp paired end reads. Paired-end reads were harvested from Illumina Hiseq-4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software(v1.9.3), the high quality clean reads were aligned to the reference genome (susScr3) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profies of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.

value: germ cells

tag: cell population

value: SSEA4-positive spermatogonia

tag: age

value: 90 days


title: SSEA4+P-S5


title: SSEA4+P-S4


title: MEC12_S5_L004: GMECs

city: Guangxi

first: ben

last: huang

address: NO.100. DAXUE EAST RD, Nanning

institute: School of Animal Science and Technology, Guangxi University

data_processing:
Illumina seqencing reads were cleaned for quality control and tested the results using FastQC(version0.10.1).
Cell Ranger count generated the matrices used in the next analysis step.was used to perform alignment, filtering, barcode counting, and UMI counting of each sample
Cellranger aggr pipline was used to combine data from samples of 3 different periods into a new feature-barcode matrix for downstream ananlysis.
Genome_build: CaprahircusARS1
Supplementary_files_format_and_content: xls files include UMI counting values for each Sample ...

organism: Capra hircus

source_name: Naturally derived mammary epithelial cells

extract_protocol:
Cells were washed using PBS, and digested with 0.25% trypsin to generate single cell suspension
Library generated following the manufacturer’s introduction of a Single Cell 3′ Library and Gel Bead Kit V2 (10x Genomics,CG00052 Rev B). Cell suspensions were loaded onto a Chromium Single-Cell Controller (10x Genomics, San Francisco, CA) to generate single-cell gel beads in an emulsion.

treatment_protocol: GEFs were seeded at a density of 5×104 cells per well of a 4-well plate or 5×105 cells per 60 mm dish and cultured in the incubator at 37.5°C in a humidified atmosphere of 5% CO2 with fibroblast culture medium. The next day, the fibroblast medium was replaced by BFRTV induction medium. The culture was continued for 8 days, and the induction medium was refreshed every 2 days. On day 8, those induced cells with primary colonies were named BFRTV-8d cells/CiMECs-P0 and were further passaged at a ratio of 1:3 every 3-4 days; the cells were cultured in the incubator at 37.5°C in a humidified atmosphere of 5% CO2 with goat MEC culture medium changed every 2 days. The culture plates or dishes were precoated with Matrigel® Matrix (Corning, 356230).

tag: induction time


title: MEC12_S5_L001: GMECs

value: Naturally derived mammary epithelial cells


title: DF88d_S3_L003: BFRTV8d

source_name: Induced mammary epithelial cell

value: Induced mammary epithelial cell


title: iMEC7_S6_L004: CiMECs

value: BFRTV-8d later


title: DF84d_S1_L001: BFRTV4d

source_name: Ear fibroblasts induced by BFRTV for 4d

value: Ear fibroblasts induced by BFRTV for 4d


title: DF84d_S1_L003: BFRTV4d


title: DF80d_S2_L003: BFRTV0d

source_name: Ear fibroblasts

value: Ear fibroblasts


title: DF80d_S1_L003: BFRTV0d


title: TRIM40 expressing HT-29 cells 2

description:
Microarray of TRIM40 expressing HT-29 cells 2
210728

tag: treatment

value: colon cancer cells

value: TRIM40 overexpression


title: GMEC10_1: GMECs

data_processing:
Illumina seqencing reads were cleaned for quality control and tested the results using FastQC(version0.10.1).
Ribosome RNA were removed again from clean reads
High-quality reads were mapped to the refer genome to obtain BAM files
the read count for each gene in each sample was counted by HTSeq, and the fragments per kilobase of million mapped reads (FPKM) was then calculated
Differential expression analysis was performed using DESeq2 (v1.16.1) with read count
Genome_build: CaprahircusARS1
Supplementary_files_format_and_content: xls files include FPKM values for each Sample ...

extract_protocol:
Extract total RNA from each sample,then use Ribo-Zero™ Gold Kits（Human/Mouse/Rat） to delete rRNA
RNA fragmentation and short RNA strands were carried out by NEBNext First Strand Synthesis Reaction Buffer under elevated temperature. Subsequently， First cDNA strand was synthesized using random hexamer primers and RNA fragments as template. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were  purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair、 add poly(A)and adapter were implemented. Libraries were sequenced on Illumina HiSeq 2500


title: DF80d_S1_L001: BFRTV0d


title: CiMEC7_3: CiMECs


title: GMEC10_2: GMECs


title: T cells, 15min, PBS, 2

value: healthy

value: blood


title: GMEC10_3: GMECs


title: CiMEC7_1: CiMECs


title: CiMEC7_2: CiMECs


title: 0809_DF7_5i_8d_1: BFRTV8d


title: DF84d_S3_L006: BFRTV4d


title: DF88d_S8_L003: BFRTV8d


title: 0809_DF7_5i_6d: BFRTV6d

source_name: Ear fibroblasts induced by BFRTV for 6d

value: Ear fibroblasts induced by BFRTV for 6d


title: 0809_DF7_5i_4d_1: BFRTV4d


title: 0809_DF7_5i_4d_2: BFRTV4d


title: 0809_DF7_5i_8d_2: BFRTV8d


title: 0705_DF6_5i_4d: BFRTV4d


title: 0705_DF6_5i_3d: BFRTV3d

source_name: Ear fibroblasts induced by BFRTV for 3d

value: Ear fibroblasts induced by BFRTV for 3d


title: 0705_DF6_5i_2d: BFRTV2d

source_name: Ear fibroblasts induced by BFRTV for 2d

value: Ear fibroblasts induced by BFRTV for 2d


title: 0809_DF7_5i_2d: BFRTV2d


title: 0809_DF7_5i_1d: BFRTV1d

source_name: Ear fibroblasts induced by BFRTV for 1d

value: Ear fibroblasts induced by BFRTV for 1d


title: 0705_DF6_5i_1d: BFRTV1d


title: DF6_CK: BFRTV0d


title: 0809_DF7_ck_0d_2: BFRTV0d


title: i58d3: BFRTV_8d

description: rRNA-depleted RNA

data_processing:
Illumina seqencing reads were cleaned for quality control and tested the results using FastQC(version0.10.1).
Ribosome RNA were removed again from clean reads
High-quality reads were mapped to the refer genome to obtain BAM files
the read count for each gene in each sample was counted by HTSeq, and the fragments per kilobase of million mapped reads (FPKM) was then calculated
Differential expression analysis was performed using DESeq2 (v1.16.1) with read count
Genome_build: Capra_hircus_ARS1
Supplementary_files_format_and_content: xls files include FPKM values for each Sample ...

growth_protocol: There are six samples are analyzed.BFRTV_0d are control group with three replicate. BFRTV_8d are treatment group with three replicates.

extract_protocol:
Extract total RNA from each sample,then use Ribo-Zero™ Gold Kits（Human/Mouse/Rat） to delete rRNA
RNA fragmentation and short RNA strands were carried out by NEBNext First Strand Synthesis Reaction Buffer under elevated temperature. Subsequently， First cDNA strand was synthesized using random hexamer primers and RNA fragments as template. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were  purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair、 add poly(A)and adapter were implemented. Libraries were sequenced on Illumina HiSeq Sequencing Platform.


title: i58d2: BFRTV_8d

description: rRNA-depleted RNA


title: CK2: BFRTV_0d

description: rRNA-depleted RNA


title: CK1: BFRTV_0d

description: rRNA-depleted RNA


title: CK3: BFRTV_0d

description: rRNA-depleted RNA


title: 0705_DF6_5i_8d: BFRTV8d


title: 0705_DF6_5i_6d: BFRTV6d


title: T cells, 15min, hBD2, 3

value: donor 3

value: PBMC

value: CD4/CD8 T cells


title: OreR, 2to3, mnase, 2

city: Kansas City

first: Kaelan

middle: Joseph

last: Brennan

state: MO

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

data_processing:
MNase-seq paired-end sequencing reads were aligned using bowtie2 (v.2.3.5.1) to the Drosophila melanogaster genome assembly dm6.
Aligned MNase-seq BAM files were deduplicated based on unique fragment coordinates and filtered to contain fragment lengths no greater than 600 bp.
Genome-wide fragment coverage was calculated and saved in BigWig format.
Assembly: UCSC dm6
Supplementary files format and content: BigWig

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: All embryos were collected from population cages using apple juice plates with yeast paste, following two pre-clearings. For MNase experiments, embryos were collected for 1 hour and aged for 2 hours at 25°C.

extract_protocol:
For each MNase digestion, 100 hand-sorted 2-3 h AEL Drosophila embryos were used. Nuclei were extracted by douncing in PBS with 0.1% IGEPAL CA-630. The nuclei were harvested by centrifugation and resuspended gently in MNase Digestion Buffer (PBS with 0.1% Triton X-100 and 1 mM CaCl2). MNase digestion was performed with 100 U MNase (NEB, M0247S) for 30 minutes at 37°C. The reaction was stopped with 20 mM EGTA. The nuclei were treated with 50 µg/ml RNase A (Thermo Scientific, EN0531) for 1 hour at 37 °C and 1000 rpm, and subsequently incubated overnight at 65 °C and 1000 rpm with 200 µg/ml Proteinase K (Invitrogen, 100005393) and 0.5% SDS for reverse cross-linking. DNA was extracted using phenol-chloroform (VWR, K169).
MNase-seq libraries were constructed from 10 ng purified DNA using the High Throughput Library Prep Kit from KAPA Biosystems (KK8234) according to the manufacturer’s instructions.
MNase-seq for nucleosome occupancy using standard Illumina protocols.

treatment_protocol: All embryos were dechorionated with 50% bleach for 2 minutes, rinsed with water, and fixed with 1.8% formaldehyde while vortexing for 15 minutes. Fixation was quenched with PBT-glycine (125 mM glycine in PBT) and vortexing for 2 minutes. Embryos were hand-sorted based on morphology in ice-cold PBT and then immediately used in MNase-seq experiments.

value: embryo

value: Wild-type (Oregon-R)

tag: developmental stage

value: 2-3 hours after egg laying


title: OreR, 2to3, mnase, 1


title: OreR, 2to3, mnase, 3


title: 0809_DF7_5i_3d: BFRTV3d


title: OreR, H3K27ac, seq, 1

data_processing:
ChIP-nexus reads were pre-processed by trimming off fixed and random barcodes and reassigning them to FASTQ read names.
ChIP-nexus adapter fragments were trimmed from the 3’ end of the fragments using cutadapt (v.2.5)
ChIP-nexus reads were aligned using bowtie2 (v.2.3.5.1) to the Drosophila melanogaster genome assembly dm6. Aligned ChIP-nexus BAM files were deduplicated based on unique fragment coordinates and barcode assignments.
Genome-wide coverage was calculated and saved in BigWig format.
ChIP-nexus peaks were called using MACS2 (v.2.2.7.1) with parameters designed to resimulate the full fragment length coverage rather than the single stop base coverage (--keep-dup=all -f=BAM --shift=-75 --extsize=150).
ChIP-seq reads were aligned using bowtie2 (v.2.3.5.1) to the Drosophila melanogaster genome assembly dm6. Aligned ChIP-seq BAM files were deduplicated based on unique fragment coordinates and fragments extended based on the average experiment fragment length as determined with an Agilent 2100 Bioanalyzer.
Genome-wide coverage was calculated and saved in BigWig format.
ChIP-seq peaks were called using MACS2 (v.2.2.7.1) with default parameters and an applied background coverage using the associated WCE ChIP-seq control experiment.
Assembly: UCSC dm6
Supplementary files format and content: BigWig, narrowPeak (except for Input sample)

growth_protocol: All embryos were collected from population cages using apple juice plates with yeast paste, following two pre-clearings. For ChIP experiments, embryos were collected for 1 hour and aged for 2 hours at 25°C.

extract_protocol:
For ChIP, 0.2-0.4 grams of fixed 2-3 h AEL embryos were used for all experiments. Chromatin extracts were prepared by douncing embryos in Lysis Buffer A1 (15 mM HEPES pH 7.5, 15 mM NaCl, 60 mM KCl, 4 mM MgCl2, 0.5% Triton X-100, 0.5 mM DTT (add fresh)), washing nuclei with ChIP Buffer A2 (15 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.5% N-lauroylsarcosine, 0.1% sodium deoxycholate, and 0.1% SDS), and sonicating with a Bioruptor Pico (Diagenode) for six cycles of 30 seconds on and 30 seconds off. All ChIP-nexus experiments were performed using antibodies custom generated by Genscript: Zelda (aa 1117-1327), Dorsal (aa 39-346), Twist (C-terminus), Bicoid (C-terminus), Caudal (aa 1-214), GAF (aa 1-382). ChIP-seq experiments were performed with the following commercially available antibodies: H3K27ac (Active motif, 39133) and H3K4me1 (Active motif, 39635).
ChIP-nexus was performed according to He et al., 2015, except that the ChIP-nexus adapter mix contained four fixed barcodes and PCR library amplification was performed directly after circularization of the purified DNA fragments (without addition of the oligo and BamHI digestion). ChIP-seq was performed as previously described in He et al., 2011, and included a whole cell extract (WCE).
ChIP-nexus for transcription factors and ChIP-seq for histone modifications using standard Illumina protocols.

treatment_protocol: All embryos were dechorionated with 50% bleach for 2 minutes, rinsed with water, and fixed with 1.8% formaldehyde while vortexing for 15 minutes. The vitelline membrane was removed using methanol/heptane and embryos were stored in methanol at -20°C until use.

tag: chip antibody

value: H3K27ac (Active motif, 39133)


title: OreR, H3K4me1, seq, 1

value: H3K4me1 (Active motif, 39635)


title: OreR, H3K4me1, seq, 2


title: OreR, Zld, nexus, 3

value: Custom GenScript Zld (aa 1117-1327)


title: OreR, Zld, nexus, 2


title: 0809_DF7_ck_0d_1: BFRTV0d

value: Ear fibroblasts


title: OreR, Zld, nexus, 1


title: i58d1: BFRTV_8d

description: rRNA-depleted RNA

value: Induced mammary epithelial cell


title: OreR, Twi, nexus, 3

value: Custom GenScript Twi (C-term)


title: OreR, Twi, nexus, 1


title: OreR, GAF, nexus, 1

value: Custom GenScript GAF (aa 1-382)


title: OreR, GAF, nexus, 3


title: OreR, Twi, nexus, 2


title: OreR, GAF, nexus, 2


title: OreR, Dl, nexus, 2

value: Custom GenScript Dl (aa 39-346)


title: OreR, Cad, nexus, 3

value: Custom GenScript Cad (aa 1-214)


title: OreR, Dl, nexus, 3


title: OreR, Cad, nexus, 1


title: OreR, Bcd, nexus, 3

value: Custom GenScript Bcd (C-term)


title: OreR, Bcd, nexus, 2


title: OreR, WCE, seq, 1


title: OreR, H3K27ac, seq, 2


title: OreR, Bcd, nexus, 1


title: cic6, 2.5to3, atac, 3

data_processing:
ATAC-seq paired-end sequencing reads were aligned using bowtie2 (v.2.3.5.1) to the Drosophila melanogaster genome assembly dm6.
Aligned ATAC-seq BAM files were marked for duplicates using Picard (v.2.23.8) based on unique fragment coordinates, deduplicated, reoriented according to a Tn5 enzymatic cut correction of -4/+4 on fragment ends, filtered to contain fragment lengths no greater than 600 bp, and corrected for dovetailed reads.
Genome-wide fragment coverage was calculated and saved in BigWig format.
ATAC-seq peaks were called using MACS2 (v.2.2.7.1) with default paired-end parameters using ATAC-seq fragment coverage.
The DESeq2 package (Love et al., 2014) in R was used to compute the differential chromatin accessibility in the following comparisons at all time points: wt vs. zld-; wt vs. gd7; wt vs. cic6. The differential accessibility information is provided for all comparisons as supplemental files.
Assembly: UCSC dm6
Supplementary files format and content: BigWig, narrowPeak

growth_protocol: All embryos were collected from population cages using apple juice plates with yeast paste, following two pre-clearings. For ATAC-seq, embryos were collected at 25°C in 30 minute-windows and aged accordingly to generate the 1-1.5, 1.5-2, 2-2.5, and 2.5-3 h AEL time points.

extract_protocol:
For ATAC-seq time course experiments, the following amounts of hand-sorted embryos were used: 400 embryos (1-1.5 h AEL); 100 embryos (1.5-2 h AEL); 40 embryos (2-2.5 h AEL, 2.5-3 h AEL). Following sorting, embryos were immediately dounced in ATAC Resuspension Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) with 0.1% IGEPAL CA-630 and nuclei were harvested by centrifugation. The nuclear pellet was incubated for 3 minutes on ice in ATAC resuspension buffer supplemented with 0.1% IGEPAL CA-630, 0.1% Tween-20, and 0.01% Digitonin (Promega, G9441). The reaction was stopped by adding ATAC Resuspension Buffer with 0.1% Tween-20 followed by centrifugation. Tagmentation took place at 37°C for 30 minutes at 1000 rpm in a 50 µL reaction volume containing 10 µL of 5x Tagment DNA Buffer (50 mM Tris-HCl pH 7.4, 25 mM MgCl2, 50% DMF) 16.5 µL 1x PBS, 0.5 µL 10% Tween-20, 0.5 µL 1% Digitonin, 1-2 µM assembled transposome, and water.
Accessible fragments were purified using the Monarch PCR & DNA Cleanup Kit (NEB). Libraries were constructed using Illumina Nextera Dual Indexing, and qPCR was used to prevent over-amplification as done in Corces et al., 2017.
ATAC-seq for chromatin accessibility using standard Illumina protocols.

treatment_protocol: All embryos were dechorionated with 50% bleach for 2 minutes and sufficiently rinsed with water afterwards. For ATAC-seq, embryos were hand-sorted based on morphology in ice-cold PBT immediately following dechorionation using an inverted contrasting microscope as described in Chen et al., 2013.

value: 2.5-3 hours after egg laying


title: cic6, 2.5to3, atac, 2


title: cic6, 2.5to3, atac, 1


title: cic6, 2to2.5, atac, 3

value: 2-2.5 hours after egg laying


title: cic6, 2to2.5, atac, 2


title: cic6, 2to2.5, atac, 1


title: zld-, 2.5to3, atac, 3

value: zld-


title: zld-, 2.5to3, atac, 2


title: zld-, 2.5to3, atac, 1


title: OreR, Dl, nexus, 1


title: zld-, 2to2.5, atac, 2


title: zld-, 2to2.5, atac, 1


title: OreR, Cad, nexus, 2


title: zld-, 1.5to2, atac, 3

value: 1.5-2 hours after egg laying


title: zld-, 1.5to2, atac, 2

value: embryo


title: zld-, 1to1.5, atac, 3

value: 1-1.5 hours after egg laying


title: zld-, 1.5to2, atac, 1


title: gd7, 2.5to3, atac, 1


title: gd7, 2.5to3, atac, 2


title: zld-, 1to1.5, atac, 2


title: gd7, 2to2.5, atac, 3


title: gd7, 2to2.5, atac, 1


title: gd7, 2to2.5, atac, 2


title: gd7, 1.5to2, atac, 2


title: gd7, 1.5to2, atac, 3


title: gd7, 1.5to2, atac, 1


title: gd7, 1to1.5, atac, 3


title: gd7, 1to1.5, atac, 1


title: gd7, 1to1.5, atac, 2


title: zld-, 2to2.5, atac, 3


title: OreR, 2.5to3, atac, 2

value: Wild-type (Oregon-R)


title: OreR, 2.5to3, atac, 3


title: OreR, 2.5to3, atac, 1


title: OreR, 2to2.5, atac, 1


title: OreR, 2to2.5, atac, 3


title: zld-, 1to1.5, atac, 1


title: gd7, 2.5to3, atac, 3


title: OreR, 1.5to2, atac, 1


title: OreR, 1.5to2, atac, 2


title: OreR, 1to1.5, atac, 3


title: OreR, 1to1.5, atac, 1


title: OreR, 1to1.5, atac, 2


title: P9_74

city: La Jolla

first: Klaus

last: Ley

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

data_processing:
150 bp paired-end raw sequencing reads from Illumina NovaSeq (Illumina pipeline v1.9) for 176 cells were run through FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) (v0.11.7). All cells passed sequence quality score as defined by FASTQC. On average, we captured 2.5 million reads per cell. STAR (v2.6.0a) (24) Index was built using ENSEMBL GRCm38 genome (primary assembly) and annotation (GRCm38.92) (25). Raw reads were then mapped using STAR with the added parameters ‘--quantMode GeneCounts’ and ‘--outSAMunmapped Within’. The mapped reads BAM file was sorted using SAMtools (v0.1.19) (26). Post-mapping sequencing quality was performed on the sorted BAM file using QoRTs (v1.3.0) (27). Gene body coverage was determined for the upper middle quartile genes according to QoRTs. Mapping rate includes unique as well as multi-mapping reads.
Assembly: ENSEMBL GRCm38 genome (primary assembly) and annotation (GRCm38.92)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Negative

extract_protocol:
Single cell libraries were prepared according to the Smart-Seq2-protocol (22,23) with following modifications. Pre-amplification PCR cycles were increased to 23 to obtain sufficient amounts of cDNA for the sequencing analysis. Primer dimers were eliminated by two 0.8x Ampure-XP bead clean ups. 0.3-0.5 ng of pre-amplified cDNA were subjected to library preparation with the Nextera XT library preparation kit, Illumina, San Diego, CA, USA in 8 µl reaction volume.
Barcoded libraries were pooled and sequenced the with a S1 flow cell and a 300-cycle kit on a NovaSeq Illumina platform to obtain 150-bp paired-end reads. Quality controls were performed using TapeStation with D5000 high sensitivity tapes (both from Agilent, Santa Clara, CA, USA). Quantification was performed using Qubit high sensitivity kit (Thermo Fisher Scientific) after PCR preamplification, and the PicoGreen assay (Thermo Fisher Scientific) after Nextera XT had been performed.

value: T cell

value: Negative

tag: strain


title: P9_90


title: P9_66


title: P9_53


title: P9_45


title: P9_61


title: P9_37


title: P9_3


title: P9_27


title: P9_2


title: P9_26


title: OreR, 2to2.5, atac, 2

tag: genotype


title: P9_19


title: OreR, 1.5to2, atac, 3


title: P8_63


title: P9_10


title: P9_82


title: P8_61


title: P8_82


title: P8_58


title: P8_66


title: P8_55


title: P8_45


title: P8_53


title: P8_90


title: P8_47


title: P8_74


title: P8_37


title: P9_18


title: P8_26


title: P8_39


title: P8_27


title: P8_2


title: P8_19


title: P8_50


title: P8_34


title: P9_11


title: P8_18


title: P8_10


title: P8_11


title: P7_90


title: P7_82


title: P7_66


title: P7_63


title: P7_58


title: P7_74


title: P7_50


title: P7_55


title: P7_47


title: P8_3


title: P7_39


title: P6_90


title: P7_42


title: P7_2


title: P6_9


title: P7_10


title: P6_82


title: P7_18


title: P7_26


title: P6_55


title: P6_57


title: P6_7


title: P6_58


title: P7_34


title: P6_74


title: P6_59


title: P6_50


title: P6_52


title: P6_51


title: P6_66


title: P6_49


title: P6_47


title: P6_44


title: P6_43


title: P6_41


title: P8_42


title: P6_60


title: P6_63


title: P6_4


title: P6_39


title: P6_36


title: P6_35


title: P6_34


title: P6_17


title: P6_18


title: P6_33


title: P6_26


title: P6_20


title: P6_19


title: P6_28


title: P6_15


title: P5_82


title: P6_31


title: P6_11


title: P6_42


title: P6_27


title: P6_2


title: P6_23


title: P6_10


title: P6_1


title: P5_74


title: P6_12


title: P5_90


title: P5_66


title: P5_63


title: P5_58


title: P6_3


title: P6_25


title: P5_55


title: P5_50


title: P5_47


title: P5_42


title: P5_39


title: P5_34


title: P5_26


title: P5_15


title: P5_18


title: P5_10


title: P4_63


title: P4_58


title: P4_50


title: P4_90


title: P4_74


title: P4_82


title: P5_23


title: P4_55


title: P4_47


title: P5_7


title: P4_66


title: P4_7


title: P4_31


title: P4_34


title: P4_42


title: P4_23


title: P4_26


title: P4_39


title: P4_18


title: P4_2


title: P5_31


title: P5_2


title: P4_15


title: P4_10


title: P3_90


title: P3_74


title: P3_7


title: P3_82


title: P3_66


title: P3_42


title: P3_50


title: P3_39


title: P3_4


title: P3_34


title: P3_63


title: P3_55


title: P3_26


title: P3_23


title: P3_47


title: P3_28


title: P3_20


title: P3_31


title: P3_2


title: P3_18


title: P3_15


title: P3_12


title: P3_10


title: P2_90


title: P2_82


title: P2_66


title: P2_4


title: P3_58


title: P2_26


title: P2_28


title: P2_20


title: P2_12


title: P2_18


title: P2_2


title: P2_74


title: P2_10


title: untreated, 2

city: New York

first: Ziyan

last: Lin

state: NY

department: Applied Bioinformatics Laboratories

institute: NYU Grossman School of Medicine

description: replicate 2

data_processing:
NovaSeq 6000 System (RTA Version 3.4.4)
bcl2Fastq v2.20
Trimming, alignment and generating count matrix were all done by using the sns/rna-star pipeline (https://igordot.github.io/sns/routes/rna-star.html)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Tumors were freshly isolated and processed for RNA extraction

extract_protocol:
RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit including DNASE1 treatment. Quality control was performed with Agilent Bioanalyser.
RNA-Seq library preps were constructed using the Illumina TruSeq® Stranded mRNA Library Prep kit (Cat #20020595) using 150ng of total RNA as input with 13 cycles of PCR amplification
RNA-seq: Sequencing was paired-end 50 cycles using an SP100 cycle flowcell-v1.5 on an Illumina NovaSeq6000 sequencer with 2% PhiX spike-in.

treatment_protocol:
tumor cells were inoculated 1 week before treatment start
mice were treated for 1 week with Sindbis virus vectors

value: tumor cells

value: ID8 Mouse Ovarian Surface Epithelial Cell Line

value: control

tag: time

value: 1 week


title: untreated, 1

description: replicate 1


title: SV.IgGOX40, 2

description: replicate 2

value: Sindbis expressing OX40


title: SV.IL-12, 3

description: replicate 3

value: Sindbis expressing IL-12


title: SV.IgGOX40, 1

description: replicate 1


title: SV.IgGOX40, 3

description: replicate 3


title: untreated, 3

description: replicate 3


title: SV.IL-12, 1

description: replicate 1


title: SV.IL-12, 2

description: replicate 2


title: SV, 3

description: replicate 3

value: Sindbis


title: SV, 2

description: replicate 2


title: SV.IgGOX40.IL-12, 3

description: replicate 3

value: Sindbis coexpressing OX40 and IL-12


title: SV.IgGOX40.IL-12, 1

description: replicate 1


title: SV.IgGOX40.IL-12, 2

description: replicate 2


title: SV, 1

description: replicate 1


title: Liver, IF, replicate 745

city: Stanford

first: Roel

last: Nusse

address: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Hepatocytes were isolated from livers of 8-week-old C57BL/6J mice that had been intermittent fasted for 1 week or ad libitum fed using a two-step collagenase perfusion technique.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, hepatocytes were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Liver

value: Hepatocyte

value: intermittently fasted (IF)


title: Liver, IF, replicate 744

description: 10x Genomics


title: Liver, IF, replicate 740

description: 10x Genomics


title: Liver, AL, replicate 743

description: 10x Genomics

value: ad libitum fed (AL)


title: Liver, AL, replicate 742

description: 10x Genomics


title: Liver, AL, replicate 741

description: 10x Genomics


title: DIF_NC_3

city: Wuhan

first: Xiang

last: Li

address: Youyi Road

institute: Hubei University

data_processing:
Through removing low quality, ploy-N, and adapter contained reads by in-house perl scripts, high-quality clean data were used for further analysis.
After building index of the reference genome (GRCm38), paired-end clean reads were aligned to the mouse genome using Hisat (v2.0.5).
For the quantification of gene expression, featureCounts (v1.5.0–p3) was used to count the clean reads numbers mapped to each gene, and the FPKM (fragments per kilobase of transcript per million mapped reads) value of each gene was obtained according to the gene length and reads count.
Assembly: GRCm38
Supplementary files format and content: Text file include all FPKM values for each Sample

source_name: normal differentiated cells

growth_protocol: R1 mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatin-coated dishes and maintained in KnockOutTM DMEM (Gibco) supplemented with 15% FBS (Hyclone), 1000 U/mL leukemia inhibitory factor (LIF) (Millipore), 1× MEM Non-Essential Amino Acids Solution, 1× GlutaMAXTM, 100 μM β-mercaptoethanol (Sigma-Aldrich), 100 mg/mL streptomycin (Gibco), and 100 U/mL penicillin (Gibco).

extract_protocol:
RNA was harvested using TRIzolTM Reagent (Thermo, 15596026). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, E7530S) according to manufacturer’s recommendations.

treatment_protocol: For inducing differentiation, mESCs were digested with 0.1% trypsin (Gibco), plated on dishes at a density of 7,000 ~ 8,000 cells/cm2, cultured for 24 h, washed twice with PBS (pH 7.4), and maintained in the LIF-free cell medium containing 1 μM retinoic acid (RA) for 48 h. For OGT inhibition, 25 μM Ac45SGlcNAc was used.

value: mouse embryonic stem cells

value: normal

tag: differentiation

value: RA-induced differentiation


title: DIF_5S_1

source_name: 5S treated differentiated cells

value: 5S treatment


title: DIF_5S_2


title: DIF_5S_3


title: N_5S_3

source_name: 5S treated mouse embryonic stem cells


title: N_5S_1


title: N_NC_3

source_name: normal mouse embryonic stem cells


title: N_5S_2


title: DIF_NC_1


title: N_NC_2


title: N_NC_1


title: DIF_NC_2