title: SSM2,24H,sample3,BCR

city: Shanghai

first: Kaicheng

last: Zhou

address: No.826 Zhangheng Road

institute: Fudan University School of Pharmacy

description:
Library name: BCR_B3
10X Genomics

data_processing:
Processed scRNA-seq data generated through the 10x Genomics platform underwent Cell Ranger preprocessing.
Assembly: Mouse mm10
Supplementary files format and content: gex_Cellranger_output:matrix.mtx.gz;features.tsv.gz;barcodes.tsv.gz
Supplementary files format and content: TCR/BCR:filtered_contig_annotations.csv

source_name: Pulmonary

extract_protocol:
Single-cell RNA sequencing was performed at two critical timepoints: 24 hours post primary immunization and 7 days post-secondary immunization. Pulmonary tissues were harvested and mechanically dissociated to prepare single-cell suspensions. Aliquots containing approximately 10,000 viable cells per mouse were processed through a Chromium Single Cell Controller (10X Genomics) to generate gel bead-in-emulsions (GEMs).
cDNA libraries were prepared using the Chromium Single Cell 5' Kit (v2, PN-1000165) and Single Cell V(D)J Enrichment Kit (PN-1000215), following standardized protocols for reverse transcription, cDNA amplification, and library construction. Final sequencing was conducted on an Illumina NovaSeq 6000 platform through Novogene's commercial sequencing services.

treatment_protocol: Female BALB/c mice (6-8 weeks old) received either SSM2-only or SSM2 adjuvanted with NanoCF501 using the established immunization protocol.

value: Pulmonary

value: BALB/c

tag: Sex

value: Female


title: NanoCF501/SSM2,24H,sample2,BCR

status: Public on May 21 2025

type: SRA

country: China

description:
Library name: BCR_A2
10X Genomics

library_source: other

molecule: other

organism: Mus musculus

tag: tissue

tag: strain


title: RNA_WT_PBS_rep1

city: Xiamen

first: Lanfen

last: Chen

state: Fujian

address: Xiang'an south rd, Xiang'an district

department: Life Science

institute: Xiamen University

description: Library name: WT-1

library_source: transcriptomic

data_processing:
Basecalls were performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence and low quality bases using cutadapt(v.2.6)
Clean reads were mapped to mm10 refernece genome using STAR (v.2.7.5a) .
Read counts were obtained by mapping the aligned reads to the transcripts of known genes from UCSC by using GenomicAlignments (v.1.30.0).
Differential expression analysis was performed with methods based on the negative binomial distribution in DESeq2 (v.1.34.0), using default parameters. Benjamini and Hochberg correction were used for significance tests and multiple comparisons.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts and FPKM values for each gene in each sample.

molecule: polyA RNA

source_name: WT BMDMs

growth_protocol: For BMDMs, the femur and tibia were collected from mice of each genotype, and bone marrow cells were flushed with complete DMEM containing 50 mg ml−1 streptomycin and 10% FBS. Erythrocytes were removed via treatment with red blood cell lysis buffer, and the cell suspensions were filtered through a 40-μm cell strainer for the removal of any cell clumps. The single-cell suspensions were then plated in complete DMEM with recombinant mouse M-CSF (carrier-free, 50 ng ml−1). For full differentiation of BMDMs, the cells were cultured for an additional 8 days with replacement of the medium every day. All cells were CD11b+F4/80+ when analyzed by flow cytometry.

extract_protocol:
Total RNA was isolated using RaPure Total RNA Micro Kit (Magen, R4012).
The cDNA libraries were constructed from 1 mg RNA sample using mRNA-seq Lib Prep Kit for illumina (ABclonal, RK20302) following the guidelines of the manufacturers.

treatment_protocol: BMDSs were treated with PBS or Candida albicans.

tag: cell type

value: Bone marrow derived macrophages

tag: genotype

value: WT

tag: treatment

value: PBS


title: SSM2,24H,sample2,BCR

description:
Library name: BCR_B2
10X Genomics


title: SSM2,24H,sample1,BCR

description:
Library name: BCR_B1
10X Genomics


title: M-cre-KO-CD8-3

city: China

first: Nannan

last: Xu

state: Shanghai

address: 280s chongqing road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using  fqtools
Trimmed seaence reads were mapped to GRCm39 using Hisat2
Read count extraction and normalization were performed using subread featureCounts
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes counts values for each Samples

molecule: total RNA

growth_protocol: Naïve CD8+ T cells were sorted from spleen and lymph nodes of 8-week-old MondoAfl/fl and MondoAfl/flCD4cre mice.

extract_protocol:
Total RNA was isolated using Trizol reagent.
RNA libraries were prepared using Vazyme mRNA-Seq library Prep Kit following manufacturer's protocols

treatment_protocol: Naïve CD8+ T cells from MondoAfl/fl and MondoAfl/flCD4cre mice were activated with anti-CD3/CD28 for 24 hours.

value: KO


title: NanoCF501/SSM2,24H,sample3,BCR

description:
Library name: BCR_A3
10X Genomics


title: M-cre-KO-CD8-1


title: NanoCF501/SSM2,24H,sample1,BCR

description:
Library name: BCR_A1
10X Genomics


title: SSM2,24H,sample3,TCR

description:
Library name: TCR_B3
10X Genomics

data_processing:
Processed scRNA-seq data generated through the 10x Genomics platform underwent Cell Ranger preprocessing.
Assembly: Mouse mm10
Supplementary files format and content: gex_Cellranger_output:matrix.mtx.gz;features.tsv.gz;barcodes.tsv.gz
Supplementary files format and content: TCR/BCR:filtered_contig_annotations.csv
Library strategy: TCR-Seq


title: MOLM-13, Assay 2, day2, plate 4, rep 4

city: Seattle

first: Edie

middle: I

last: Crosse

state: Washington

address: 1100 Fairview Ave N

country: USA

institute: Fred Hutchinson Cancer Center

description:
Combined compounds for plate 4, replicate 4
Assay_2_day2_plate4_rep4

data_processing:
Demultiplex reads, trim with Cutadapt, extract UMI, align with STAR, sort and index, deduplicate with UMI-tools, concatenate counts, remove batch effects with ComBat, normalize CLR.
Assembly: NA
Supplementary files format and content: Processed data files are matrices of raw read counts for all the features (cell surface proteins) for each compound treatment and replicate
Library strategy: Surface-plex, a new high-throughput technology for amplification of antibody-oligo conjugates from plates.

organism: Homo sapiens

growth_protocol: MOLM-13 cultured in compound and RPMI media (with 10% FBS and 1% P/S) at 37C and 5% atmospheric CO2

extract_protocol:
Oligos from antibody-oligo conjugates were directly amplified from cells bound with Total-Seq B antibodies.
Illumina sequencing libraries were constructed directly from the antibody-oligos with two rounds of PCR, adding TruSeq adapters.

tag: cell line

value: acute myeloid leukemia


title: NanoCF501/SSM2,24H,sample2,TCR

description:
Library name: TCR_A2
10X Genomics


title: SSM2,24H,sample1,TCR

description:
Library name: TCR_B1
10X Genomics


title: SSM2,24H,sample2,TCR

description:
Library name: TCR_B2
10X Genomics


title: MOLM-13, Assay 2, day2, plate 3, rep 4

description:
Combined compounds for plate 3, replicate 4
Assay_2_day2_plate3_rep4


title: NanoCF501/SSM2,24H,sample3,TCR

description:
Library name: TCR_A3
10X Genomics


title: NanoCF501/SSM2,Day 35,sample3

description:
Library name: N5_3
10X Genomics

library_source: transcriptomic single cell


title: NanoCF501/SSM2,Day 35,sample2

description:
Library name: N5_2
10X Genomics


title: MOLM-13, Assay 2, day1, plate 1, rep 2

description:
Combined compounds for plate 1, replicate 2
Assay_2_day1_plate1_rep2


title: OP00043_034_rep_1_72_hr

city: Yokohama

first: Imad

last: Abugessaisa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

description: Read_length : R1:100 R2:100; Index_Type : Dual;  Individual_Lane_Loading : No; Read Cycle : 101/8/8/101

data_processing:
BCL files were converted to raw sequence reads using bcl2fastq.
Fastq files were checked for quality score using FastQC.
Mapping of the raw seq reads was performed with STAR aligner 7.1. Raw reads were mapped to the Galleria mellonella Genome assembly CSIRO_AGI_GalMel_v1 (NCBI RefSeq assembly GCF_026898425.1).
Read count summarization was done with FeatureCount Subread R package.
Assembly: NCBI RefSeq assembly GCF_026898425.1
Supplementary files format and content: Tab-delimited text file includes normalized counts (logCPM) for all samples.
Supplementary files format and content: Tab-delimited text file includes raw counts for all samples.

organism: Galleria mellonella

source_name: hemolymph

extract_protocol:
RNeasy Mini Kit (Qiagen, Germany), RNA isolation was done according to the manufacturer's instructions.
NEBNext Ultra II RNA Library Prep.

treatment_protocol: The larvae was treated with Iron(II) chloride (FeCl2) and Iron(III) chloride (FeCl3) to a final concentration of 25 µM to create an iron overload, and 332 µM ethylenediamine-N,N'-diacetic acid (EDDA) to create an iron deficit.

value: hemolymph

value: Ctrl

tag: infection

value: Madurella mycetomatis MM55

tag: time point

value: 72 hr


title: OP00043_033_rep_3_72_hr


title: NanoCF501/SSM2,Day 35,sample1

description:
Library name: N5_1
10X Genomics


title: OP00043_032_rep_2_72_hr


title: SSM2,Day 35,sample2

description:
Library name: R3_2
10X Genomics


title: OP00043_035_rep_2_72_hr


title: NanoCF501/SSM2,24H,sample1,TCR

description:
Library name: TCR_A1
10X Genomics


title: NanoCF501/SSM2,24H,sample3

description:
Library name: A3
10X Genomics


title: OP00043_030_rep_3_72_hr

value: EDDA


title: SSM2,Day 35,sample3

description:
Library name: R3_3
10X Genomics


title: SSM2,Day 35,sample1

description:
Library name: R3_1
10X Genomics


title: OP00043_031_rep_1_72_hr


title: OP00043_029_rep_2_72_hr


title: OP00043_028_rep_1_72_hr


title: SSM2,24H,sample3

description:
Library name: B3
10X Genomics


title: OP00043_027_rep_3_24_hr

value: 24 hr


title: NanoCF501/SSM2,24H,sample2

description:
Library name: A2
10X Genomics


title: SSM2,24H,sample2

description:
Library name: B2
10X Genomics


title: OP00043_036_rep_3_72_hr


title: NanoCF501/SSM2,24H,sample1

description:
Library name: A1
10X Genomics


title: SSM2,24H,sample1

description:
Library name: B1
10X Genomics


title: OP00043_025_rep_1_24_hr


title: OP00043_026_rep_2_24_hr


title: Replicate 2 for P28 cortex ALM interneuron

city: Cambridge

first: Min

last: Dai

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute of MIT and Harvard

library_source: genomic single cell

data_processing:
Reads from scATAC-seq libraries (FASTQ files) were aligned to the mouse mm10 (GENCODE vM23/Ensembl98) reference genome provided by 10x Genomics and the the fragment file was produced with the Cell Ranger ATAC pipeline v2.1.0 (10x Genomics) with default parameters (cellranger-atac count).
Assembly: mm10
Supplementary files format and content: The "filtered_peak_bc_matrix.h5" files contain the cell x peak matrices ouput by CellRanger-ATAC. The "fragments.tsv.gz" files contain the fragment files generated by CellRanger-ATAC. The "fragments.tsv.gz.tbi" files are the index files for corresponding "fragments.tsv.gz" files.

molecule: genomic DNA

source_name: Cortex - ALM

extract_protocol:
For P28 ALM (Dlx6a-cre::INTACT) scATAC-seq data, brains were collected, sectioned coronally on a stainless-steel mouse brain slicer (Zivic Instruments), and regions of interest were dissected in ice-cold ACSF. Tissue was then transferred to a Dounce homogenizer containing lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, and 0.01% IGEPAL CA-630, 0.001% digitonin). Tissue was homogenized with 10 strokes of pestle A, 10 strokes of pestle B, and incubated for 5 min on ice before being filtered through a 30 μm filter and centrifuged at 500g for 10 min at 4 °C. The pellet was resuspended in 1% BSA in PBS for sorting for GFP+ nuclei.
Nuclei were sorted into diluted nuclei buffer (10x Genomics) on a Sony SH800S cell sorter with a 100 µm chip. The scATAC-seq library was prepared using the 10x Genomics platform with the Chromium Single Cell ATAC Library & Gel Bead Kit v.1.0 (PN-1000111), Chromium Chip E Single Cell kit (PN-1000156) and Chromium i7 Multiplex Kit N, Set A (PN-1000084) as per manufacturer’s instructions. Libraries were sequenced using a Nova-Seq S2 100 cycle kit (Illumina).

value: Cortex - ALM

value: cortical interneuron


title: Replicate 1 for P28 cortex ALM interneuron


title: OP00043_022_rep_1_24_hr


title: XX_D4_scRNAseq_rep2_dFtxXert

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

description:
filtered_counts.tsv
ChrX_filtered_counts_B6.tsv
ChrX_filtered_counts_Cast.tsv
filtered_cell_info.tsv
filtered_cell_chrX_info.tsv

data_processing:
Sequencing reads from the 10x cDNA library were mapped to the mouse mm10 genome with STARsolo (v.2.7.11a) with settings [soloType=CB_UMI_Simple, soloFeatures=GeneFull_Ex50pAS](Kaminow et al. 2021; Dobin et al. 2013). To map reads to either the reference B6 or the alternative Cast alleles, the “Diploid Genome” options of STARsolo were used together with experimentally determined single nucleotide variants from the TX1072 cell line(Barros de Andrade E Sousa et al. 2019).
To remove empty droplets and assign a quality metric to the mapping of allelic reads EmptyDrops(Lun et al. 2019) and WASP(van de Geijn et al. 2015) were used within STARsolo (v.2.7.11a)(Kaminow et al. 2021).
Outlier cells were filtered using default settings of scater (v1.26.1)(McCarthy et al. 2017).
MULTI-seq sample barcodes were extracted from the separately sequenced MULTIseq library and assigned to cells using deMULTIplex2 (v1.0.1)(Zhu et al. 2024).
To generate allele-specific count tables of X-chromosomal reads, reads were filtered for high-quality assignments by the presence of the vW:i:1 WASP filter read tag. Next, X-chromosomal reads were extracted and split into separate .bam files for each haplotype. The .bam files were sorted and indexed with samtools (v1.19.2)(Li et al. 2009).
Count tables were generated using featureCounts (v2.0.6)(Liao et al. 2014) to assign reads to genes and UMI-tools (v1.1.4) to quantify UMI-level counts with option [--per-gene --gene-tag=XT --assigned-status-tag=XS --per-cell --umi-tag=CB --cell-tag=CB –extract-umi-method=tag](Smith et al. 2017). Non-allelic count tables were generated in the same manner, using the unfiltered .bam file as input.
Further downstream analyses were performed with Scanpy (v1.9.8) and Anndata (v0.10.5)(Wolf et al. 2018; Virshup et al. 2021). Cells with ≥3% mitochondrial reads were removed. Read counts were normalized to 10,000 reads per cell and log-transformed using the [sc.pp.normalize_total] and [sc.pp.log1p] functions.
To filter XO cells, cells with normalized Xist expression ≤0.5 and an X-chromosomal ratio (B6 chrX reads/total chrX reads) ≥0.85 or ≤0.15 were removed.
Assembly: mm10
Supplementary files format and content: Count tables of filtered cells (.tsv)
Supplementary files format and content: ChrX allelic count tables of filtered cells (.tsv)
Supplementary files format and content: General and chrX-specific info for filtered cells (.tsv)

source_name: Embryonic stem cells

growth_protocol: TX1072 mESCs were cultured on 0.1% gelatin-coated flasks in serum-containing medium supplemented with LIF (SL conditions) (DMEM (Sigma), 15% ESC-grade FBS (GIBCO), 0.1 mM b-mercaptoethanol, 1000 U/ml LIF (Millipore), 3 mM Gsk3 inhibitor CT-99021, 1 mM MEK inhibitor PD0325901 (Axon)). The cells were cultured at a density of 4*10^4 cells/cm2 and passaged every second day.

extract_protocol:
For sample multiplexing, MULTI-seq barcode-lipid complexes were used according to the published protocol with minor modifications(McGinnis et al. 2019). Sample barcodes were chosen from a list of compatible barcodes(Rosen et al. 2022). Lipid-modified anchor and co-anchor oligos were purchased from Sigma-Aldrich. Barcode- and library preparation oligos were purchased from Eurofins with NGSgrade quality. Per sample, 1*105 cells were transferred to a 96-well ultra-low attachment plate (Costar) and kept on ice during the procedure. After two washes with PBS, the cells were incubated 5-10 min with an Anchor:Barcode solution (45 µl PBS, 5 µl Anchor:Barcode). The mixture was incubated for another 5-10 min after adding 5 µl of Co-Anchor solution. Labeling was quenched by adding 1% BSA in PBS, samples washed once in the same solution and resuspended in 0.4% BSA in PBS. Afterwards, cells were counted, pooled equally, and filtered using a Flowmi cell strainer 40 µm (Sigma-Aldrich). 2.5*104 cells were used for scRNA-seq gene expression library preparation .
The 10x Genomics library preparation protocol was performed according to manufacturer’s instructions (CG000315 Rev E, 10X Genomics) with the additional steps required to generate the separate MULTI-seq libraries for the sample-to-cell barcode assignment(McGinnis et al. 2019). During cDNA amplification, 0.5 µL of 1.25 μM “MULTI-seq additive primer” was added. 50% of the purified gene expression cDNA was carried forward, and the cycle number in the index PCR was reduced by one accordingly, to increase library complexity(Bolondi et al. 2024). During the first step of cDNA cleanup the supernatant was kept, which contained the short MULTI-seq library. This MULTI-seq library was then cleaned up two times using SPRI beads (KAPA HyperPure Beads, Roche). Sequencing adapters containing indexes (“TruSeq_RPIX_”, and “Universal_I5_with_index”) were added by PCR, using 2.5 µL primer at 10 µM each, 10 ng of cDNA, 26.25 µL Kapa HiFi HotStart ReadyMix 2x, and water to 50 µL final volume, with a program of 95 °C 5 min, 11 cycles of 98 °C 15 sec, 60 °C 30 sec, 72 °C 30 sec; followed by 72 °C 1 min and 4 °C hold. The resulting sequencing library was then cleaned up another time with SPRI beads. 10X gene expression libraries and MULTI-seq libraries were sequenced asynchronous 90/28 bp paired-end on the NovaSeq 6000 platform.

treatment_protocol: Differentiation was induced at a density of 2.1*10^4 cells/cm2 on 10 µg/ml fibronectin (Merck or Corning) via 2i/LIF withdrawal (-2iL conditions) (DMEM, 10% FBS (GIBCO), 0.1 mM b-mercaptoethanol). Cells were harvested after 4 days.

value: Embryonic stem cells

value: TX1072 XX dFtx-Xert -/-

value: CAST / C57BL/6


title: XX_D4_MULTIseq_rep2_dFtxXert


title: OP00043_021_rep_3_24_hr


title: XX_D4_MULTIseq_rep2_WT

value: TX1072 XX A3


title: OP00043_019_rep_1_24_hr


title: XX_D4_scRNAseq_rep2_WT


title: XX_D4_MULTIseq_rep1_dFtxXert


title: OP00043_017_rep_2_4_hr

value: 4 hr


title: XX_D4_scRNAseq_rep1_dFtxXert


title: XX_D4_MULTIseq_rep1_WT


title: OP00043_015_rep_3_4_hr


title: OP00043_014_rep_2_4_hr


title: OP00043_016_rep_1_4_hr


title: RNA_XO_96h_R2

description:
Counts_RNA_timecourse.txt
CPM_RNA_timecourse.txt
DEseq2_total.txt

data_processing:
Reads were aligned to the mouse reference genome (mm10) using STAR (v2.7.9a) with options [--outSAMattributes NH HI NM MD](Dobin et al. 2013).
The data was filtered for mapped and paired reads and sorted using samtools (v1.10) with options [view -f 3 -q 7] and [sort](Li et al. 2009).
Gene expression was quantified using the GENCODE M25 annotation supplemented with the Xert coordinates(Frankish et al. 2019; Gjaltema et al. 2022). Here, Rsubread (v2.0.1) was used with the options [featureCounts(isPaiedEnd=TRUE, GTF.featureType=”exon”, strandSpecific=2](Liao et al. 2019).
Differential expression between the cell lines at individual time points was quantified using DESeq2 (Wald.FDR≤0.05) (Love et al. 2014).
Assembly: mm10
Supplementary files format and content: Count tables (.txt)
Supplementary files format and content: Normalized counts (.txt
Supplementary files format and content: Differential expression (.txt)

growth_protocol: TX1072 mESCs were cultured on 0.1% gelatin-coated flasks in serum-containing medium supplemented with 2i and LIF (2iSL conditions) (DMEM (Sigma), 15% ESC-grade FBS (GIBCO), 0.1 mM b-mercaptoethanol, 1000 U/ml LIF (Millipore), 3 mM Gsk3 inhibitor CT-99021, 1 mM MEK inhibitor PD0325901 (Axon)). The cells were cultured at a density of 4*104 cells/cm2 and passaged every second day.

extract_protocol:
RNA was isolated using Trizol and the Direct-zol RNA Miniprep kit (Zymo research).
PolyA-enriched RNA-seq was performed using the Collibri Stranded RNA Library Prep Kit (Thermo Fisher).

treatment_protocol: Differentiation was induced at a density of 2.1*10^4 cells/cm2 on 10 µg/ml fibronectin (Merck or Corning) via 2i/LIF withdrawal (-2iL conditions) (DMEM, 10% FBS (GIBCO), 0.1 mM b-mercaptoethanol).


title: RNA_XO_96h_R3


title: OP00043_013_rep_1_4_hr


title: XX_D4_scRNAseq_rep1_WT


title: RNA_XO_96h_R1


title: OP00043_023_rep_2_24_hr


title: OP00043_012_rep_3_4_hr


title: RNA_XO_72h_R1


title: OP00043_010_rep_1_4_hr


title: OP00043_009_rep_3_0_hr

value: 0 hr


title: OP00043_024_rep_3_24_hr


title: RNA_XO_72h_R2


title: RNA_XO_72h_R3


title: OP00043_011_rep_2_4_hr


title: OP00043_020_rep_2_24_hr


title: RNA_XO_56h_R3


title: OP00043_007_rep_1_0_hr


title: RNA_XO_56h_R1


title: RNA_XO_56h_R2


title: OP00043_018_rep_3_4_hr


title: OP00043_008_rep_2_0_hr


title: OP00043_006_rep_3_0_hr


title: RNA_XO_48h_R1


title: RNA_XO_48h_R2


title: OP00043_004_rep_1_0_hr


title: OP00043_003_rep_3_0_hr


title: OP00043_002_rep_2_0_hr


title: RNA_XO_36h_R2


title: RNA_XO_36h_R3


title: OP00043_001_rep_1_0_hr


title: RNA_XO_30h_R1


title: RNA_XO_30h_R3


title: RNA_XO_24h_R2


title: RNA_XO_24h_R3


title: RNA_XO_24h_R1


title: RNA_XO_16h_R2


title: RNA_XO_10h_R1


title: RNA_XO_10h_R2


title: RNA_XO_10h_R3


title: RNA_XO_0h_R3


title: RNA_XO_16h_R1


title: RNA_XO_0h_R1


title: RNA_XX_96h_R1


title: RNA_XX_72h_R2


title: RNA_XX_72h_R3


title: OP00043_005_rep_2_0_hr


title: RNA_XO_48h_R3


title: RNA_XX_96h_R2


title: RNA_XX_72h_R1


title: RNA_XX_96h_R3


title: RNA_XX_56h_R3


title: RNA_XO_16h_R3


title: RNA_XO_30h_R2


title: 5-hCD8-LA

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim galore
Trimmed seaence reads were mapped to GRCh38 using Hisat2
Read count extraction and normalization were performed using subread featureCounts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Samples

source_name: PBMC

growth_protocol: Naïve CD8+ T cells were sorted from healthy human PBMC and activated with anti-CD3/CD28 beads in X-VIVO T-cell culture medium.

treatment_protocol: CD8+ T cells were treated with or without 10 mM lactic acid for 24 hours.

value: PBMC

value: Lactic acid


title: RNA_XO_0h_R2


title: RNA_XX_56h_R1


title: 4-hCD8-LA


title: 3-hCD8-LA


title: RNA_XX_56h_R2


title: RNA_XX_48h_R1


title: 2-hCD8-LA


title: 1-hCD8-LA


title: 5-hCD8-Ctrl


title: RNA_XX_48h_R3


title: RNA_XX_48h_R2


title: RNA_XX_36h_R3


title: RNA_XX_36h_R2


title: 3-hCD8-Ctrl


title: RNA_XX_30h_R3


title: RNA_XX_36h_R1


title: 2-hCD8-Ctrl


title: 4-hCD8-Ctrl


title: 1-hCD8-Ctrl


title: RNA_XX_30h_R2


title: 4-h-iTreg-LA-24h

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim galore
Trimmed seaence reads were mapped to GRCh38 using Hisat2
Read count extraction and normalization were performed using subread featureCounts
Assembly: GRCh38
Supplementary files format and content: rpkm.txt (tab-delimited text file includes RPKM values for each Sample)

growth_protocol: CD4+ T cells were isolated from healthy human PBMC and cultured with anti-CD3/CD28 beads in iTreg polarization condition for 5 days.

treatment_protocol: Treg cells were treated with or without 10 mM lactic acid

value: Treg


title: 5-h-iTreg-LA-24h


title: RNA_XX_30h_R1


title: 3-h-iTreg-LA-24h


title: 2-h-iTreg-LA-24h


title: 1-h-iTreg-LA-24h


title: RNA_XX_24h_R1


title: RNA_XX_16h_R3


title: 5-h-iTreg-LA-0h


title: RNA_XX_16h_R2


title: 4-h-iTreg-LA-0h


title: RNA_XX_16h_R1


title: 3-h-iTreg-LA-0h


title: RNA_XX_10h_R3


title: 2-h-iTreg-LA-0h


title: RNA_XX_10h_R2


title: 1-h-iTreg-LA-0h


title: RNA_XX_10h_R1


title: MCF-7, biol rep3, 8h post-ActD treatment

city: Los Angeles

first: Xinshu

middle: Grace

last: Xiao

state: CA

address: 610 Charles E. Young Drive South

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

description: MCF7gDNA_S1_L006.8h.ASE_test_results.txt

data_processing:
Adapters were trimmed from reads using bbduk (tpe tbo ktrim=r k=23 mink=11 hdist=1) and then mapped using STAR-2.7.8a (--twopassMode Basic --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 10  --outFilterMismatchNoverReadLmax 0.04 --alignEndsType Local  --sjdbScore 2  --waspOutputMode SAMtag)
Read counts were obtained at heterozygous SNV positions
Testable SNVs were evaluated for allele-specific expression (ASE) using the method described in PMID: 30902979.
Assembly: hg38
Supplementary files format and content: tab-delimited file includes ASE test results per SNV for each condition (cell line, timepoint)

growth_protocol: HCT116 cells were maintained in Gibco™ McCoy’s 5A (Modified) Medium with 10% FBS (Gibco, Cat# 26140079) and antibiotic-antimycotic reagent (Gibco, Cat# 15240062) at 37°C with 5% CO2 supply. MCF-7 cells were maintained in DMEM Medium with 10% FBS (Gibco, Cat# 10569010) and antibiotic-antimycotic reagent (Gibco, Cat# 15240062) at 37°C with 5% CO2 supply. GM12878 cells were grown in RPMI 1640 (Thermo Fisher Scientific, Cat# 61870036) supplemented with 15% FBS (Gibco, Cat# 26140079) and antibiotic-antimycotic reagent (Gibco, Cat# 15240062) at 37°C with 5% CO2 supply.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep Plus kit (Zymo Research, Cat# R2072) following the manufacturer’s protocol.
Stranded mRNA (PolyA) RNA-seq libraries were prepared by the Technology Center for Genomics & Bioinformatics (TCGB) core at UCLA.

treatment_protocol: Cells were treated with 10ng/ml (GM12878 and HCT116) or 5ng/ml (MCF-7) Actinomycin D for different time points (2h, 8h, and 24h).

value: mammary gland, adenocarcinoma

value: 8h post-ActD


title: MCF-7, biol rep2, 8h post-ActD treatment


title: RNA_XX_0h_R2


title: RNA_XX_0h_R3


title: MCF-7, biol rep3, 2h post-ActD treatment

description: MCF7gDNA_S1_L006.2h.ASE_test_results.txt

value: 2h post-ActD


title: MCF-7, biol rep2, 2h post-ActD treatment


title: RNA_XX_0h_R1


title: RNA_XX_24h_R3


title: RNA_XX_24h_R2


title: MCF-7, biol rep2, 24h post-ActD treatment

description: MCF7gDNA_S1_L006.24h.ASE_test_results.txt

value: 24h post-ActD


title: MCF-7, biol rep3, 24h post-ActD treatment


title: MCF-7, biol rep3, 0h ActD (pre-treatment)

description: MCF7gDNA_S1_L006.0h.ASE_test_results.txt


title: MCF-7, biol rep2, 0h ActD (pre-treatment)


title: MCF-7, biol rep1, 2h post-ActD treatment


title: XX_D2_REPi_RE127_GFP-High_R3

description:
REPi.count.txt
REPi.count_normalized.txt
REPi_interaction_scores.txt

library_source: genomic

data_processing:
*library strategy: Pooled CRISPR screen
Count tables were generated using MAGeCK (v0.5.9.3) with [mageck count –norm-method control](Li et al. 2014).
39 Guides with low expression in the unsorted population (≤150 mean normalized counts) were removed from the analysis. Guides targeting Zfp866 were removed from the analysis since their sequence overlapped with guides targeting Gm20422. Only guides with more than 150 mean counts in the unsorted samples were used for analysis.
The noRE reporter screen was analyzed separately in order to identify interactions of targeted TFs with the FIREWACh minimal promoter. Significant enrichment or depletion was detected using an unpaired t-test between the normalized counts in the GFPHigh and GFPLow populations, followed by multiple testing correction (FDR<0.2). 7 TF targets (Nfrkb, Sall4, Ctcf, Zfp296, Zfp236, Sp1 and E2f4)  were removed from further analysis due to their effect on the noRE reporter line.
Interaction scores for the assayed TF-RE interactions were calculated as z-scores across all GFPHigh/GFPLow log2 fold changes, as done before for CRISPR screen data(Xu et al. 2021). This was done to correct for differences in observed effect sizes between the reporter lines. In detail, mean GFPHigh/GFPLow log2 fold changes were calculated for all guide/reporter combinations. Each log2 fold change was then normalized by subtracting the mean log2 fold change across each target from the noRE reporter results. The corrected fold changes were scaled using a z-score transformation and determined as interaction scores. Significance was calculated using a one-sample t-test with [t.test(mu=0)], followed by multiple testing correction with [p.adjust()].
Assembly: mm10
Supplementary files format and content: Count tables (.txt)
Supplementary files format and content: Normalized count tables (.txt)
Supplementary files format and content: Interaction scores (.txt)

growth_protocol: TX1072 SP107 mESCs were cultured on 0.1% gelatin-coated flasks in serum-containing medium supplemented with 2i and LIF (2iSL conditions) (DMEM (Sigma), 15% ESC-grade FBS (GIBCO), 0.1 mM b-mercaptoethanol, 1000 U/ml LIF (Millipore), 3 mM Gsk3 inhibitor CT-99021, 1 mM MEK inhibitor PD0325901 (Axon)). The cells were cultured at a density of 4*104 cells/cm2 and passaged every second day.

extract_protocol:
Following cell sorting at the FACS, genomic DNA was isolated using phenol/chloroform extraction. First, cell pellets were incubated for 14 hours at 65 °C in de-crosslinking buffer (1% SDS (Invitrogen), 1.25 µl DTT (Roth) and 10 µl 5M NaCl (Sigma) in Tris-EDTA buffer (Sigma)). Next, 20 µl RNAse A (10 mg/ml, New England Biolabs) were added and the solution incubated for 1 hour at 37 °C. Following, 5 µl Proteinase K (20 mg/ml, Ambion) was added and the solution incubated for 1 hour at 50 °C. Subsequently, 275 µl of Phenol/Chloroform (Roth) were added and the mixture vortexed for 1 min. The samples were then centrifuged for 10 min at 13,000 rpm. The aqueous phase, containing the genomic DNA, was transferred to a new tube and the sample was cleaned using ethanol precipitation. The pellets were dried and resuspended in 50 µl water.
The guide cassette was amplified for 20-25 cycles using the KAPA HiFi PCR ReadyMix with primers OG115/OG116. At least 2.2 µg of genomic DNA were amplified per sample. Following clean-up with the DNA Clean & Concentrator Kit, sequencing barcodes were added in a second PCR using the KAPA HiFi PCR ReadyMix for 9-11 cycles

treatment_protocol: The cells were transduced with a lentiviral CRISPRi library and selected for integrations using puromycine. Differentiation was induced at a density of 2.1*104 cells/cm2 on 10 µg/ml fibronectin (Merck or Corning) via 2i/LIF withdrawal (-2iL conditions) (DMEM, 10% FBS (GIBCO), 0.1 mM b-mercaptoethanol). Knockdown was induced 1 days prior to differentiation via the addition of 100 µM ABA to the medium.

value: 2iL-withdrawal/Pooled CRISPRi screen


title: XX_D2_REPi_RE127_GFP-Low_R2


title: XX_D2_REPi_RE127_GFP-Low_R3


title: XX_D2_REPi_RE127_GFP-High_R2


title: XX_D2_REPi_RE127_Unsorted_R3


title: XX_D2_REPi_RE127_GFP-Low_R1


title: HeLa cells,pIRF3(input),linear pcDNA3.1-neo,rep3 (ChIP-seq)

city: Hong Kong

first: yicen

last: zhou

address: Block 2, To Yuen Building, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

data_processing:
ChIP-seq data were aligned to the reference genome hg19 using Bowtie2 (2.5.1).
After removing duplicates using the MarkDuplicates command of Picard (3.1.1), peaks were called from the bam files by MACS2 (2.2.9.1).
The bam files of biological replicates were merged by samtools (1.17).
BigWig files were obtained using the bamCoverage command with –normalizeUsing RPKM option from deeptools (3.5.1).
Assembly: hg19
Supplementary files format and content: bigWig

source_name: HeLa

growth_protocol: plasmid of linear pcDNA3.1-neo  were transfected into HeLa cells grown on the 6-well plates, and incubated for 24h

extract_protocol:
1% Formaldehyde (Sigma, F8775) was added into each well to crosslink the cells for 10 min with a slight shaking at room temperature.chromtin was sonicated using Covaris M220 sonicator.
DNA was isolated by performing a phenol/chloroform/isoamyl alcohol extraction to prepare the ChIP-seq library using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645).

value: HeLa

value: human cervical adenocarcinoma cell

tag: chip antibody

value: transfected with linear pcDNA3.1-neo plasmid


title: XX_D2_REPi_RE127_GFP-High_R1

value: Embryonic stem cells


title: XX_D2_REPi_RE127_Unsorted_R2


title: HCT116, biol rep3, 8h post-ActD treatment

description: HCT116gDNA_S2_L006.8h.ASE_test_results.txt

value: colorectal carcinoma


title: MCF-7, biol rep1, 0h ActD (pre-treatment)


title: HCT116, biol rep2, 8h post-ActD treatment


title: XX_D2_REPi_RE127_Unsorted_R1

value: CAST / C57BL/6


title: MCF-7, biol rep1, 8h post-ActD treatment


title: HeLa cells,pIRF3(input),linear pcDNA3.1-neo,rep2 (ChIP-seq)


title: HeLa cells,pIRF3(input),linear pcDNA3.1-neo,rep1 (ChIP-seq)


title: HCT116, biol rep1, 8h post-ActD treatment


title: HCT116, biol rep2, 2h post-ActD treatment

description: HCT116gDNA_S2_L006.2h.ASE_test_results.txt


title: HeLa cells,pIRF3(input),control,rep3 (ChIP-seq)

value: control


title: XX_D2_REPi_RE97_GFP-Low_R3


title: XX_D2_REPi_RE97_GFP-High_R3


title: MCF-7, biol rep1, 24h post-ActD treatment


title: HCT116, biol rep1, 2h post-ActD treatment


title: HeLa cells,pIRF3(input),control,rep2 (ChIP-seq)


title: HCT116, biol rep3, 24h post-ActD treatment

description: HCT116gDNA_S2_L006.24h.ASE_test_results.txt


title: GM12878, biol rep3, 8h post-ActD treatment

description: GM12878gDNA_S3_L006.8h.ASE_test_results.txt

value: B-lymphocyte, lymphoblastoid


title: HCT116, biol rep2, 24h post-ActD treatment


title: XX_D2_REPi_RE97_Unsorted_R3


title: XX_D2_REPi_RE97_Unsorted_R2


title: XX_D2_REPi_RE97_GFP-Low_R1


title: GM12878, biol rep3, 2h post-ActD treatment

description: GM12878gDNA_S3_L006.2h.ASE_test_results.txt


title: HeLa cells,pIRF3(input),control,rep1 (ChIP-seq)


title: XX_D2_REPi_RE97_GFP-Low_R2


title: HCT116, biol rep3, 0h ActD (pre-treatment)

description: HCT116gDNA_S2_L006.0h.ASE_test_results.txt


title: XX_D2_REPi_RE97_GFP-High_R1


title: HeLa cells,pIRF3(IP),linear pcDNA3.1-neo,rep3 (ChIP-seq)

value: Phospho-IRF-3 (Ser396)(4D4G) Rabbit mAb #4947


title: XX_D2_REPi_RE97_GFP-High_R2


title: HCT116 biol rep1, 0h ActD (pre-treatment)


title: HCT116, biol rep2, 0h ActD (pre-treatment)


title: HeLa cells,pIRF3(IP),linear pcDNA3.1-neo,rep2 (ChIP-seq)


title: GM12878, biol rep2, 8h post-ActD treatment


title: HCT116, biol rep3, 2h post-ActD treatment


title: GM12878, biol rep2, 24h post-ActD treatment

description: GM12878gDNA_S3_L006.24h.ASE_test_results.txt


title: XX_D2_REPi_RE97_Unsorted_R1


title: GM12878, biol rep1, 24h post-ActD treatment


title: GM12878, biol rep3, 24h post-ActD treatment


title: GM12878, biol rep1, 2h post-ActD treatment


title: GM12878, biol rep2, 2h post-ActD treatment


title: HeLa cells,pIRF3(IP),control,rep2 (ChIP-seq)


title: HCT116, biol rep1, 24h post-ActD treatment


title: GM12878, biol rep1, 8h post-ActD treatment


title: HeLa cells,IRF7(input),linear pcDNA3.1-neo,rep3 (ChIP-seq)


title: HeLa cells,pIRF3(IP),control,rep3 (ChIP-seq)


title: HeLa cells,pIRF3(IP),linear pcDNA3.1-neo,rep1 (ChIP-seq)


title: XX_D2_REPi_RE96_GFP-Low_R3


title: roots, CK-WT-3-RNA-seq

city: Guangzhou

first: Guoxuan

last: Liu

address: Wushan

institute: 华南农业大学

data_processing:
Illumina Casava software used for basecalling.
（1）Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted )（2）Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality).（3）Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%)
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
The GO （Gene Ontology, http://geneontology.org/）enrichment of DEGs was implemented by the hypergeometric test. GO terms with q<0.05 were considered to be significantly enriched.The KEGG PATHWAY enrichment of DEGs was implemented by the hypergeometric test. KEGG terms with q<0.05 were considered to be significantly enriched. genome build
Assembly: soybean (downloaded from ENSEMBL database (http://www.ensembl.org/index.html))
Supplementary files format and content: tab-delimited text files include raw counts for each Sample .
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

organism: Glycine max

source_name: roots

extract_protocol:
RNA was extracted from the sample by using Trizol Reagent (Invitrogen) , and then the RNA sample was strictly controlled.RNA purity was detected by NanoPhotometer® spectrophotometer (Thermo Fisher). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina NR604-01/02,

value: roots

value: WT

value: CK


title: HeLa cells,pIRF3(IP),control,rep1 (ChIP-seq)


title: XX_D2_REPi_RE96_GFP-High_R3


title: GM12878, biol rep3, 0h ActD (pre-treatment)

description: GM12878gDNA_S3_L006.0h.ASE_test_results.txt


title: roots, CK-WT-1-RNA-seq


title: GM12878, biol rep2, 0h ActD (pre-treatment)


title: HeLa cells,IRF7(input),linear pcDNA3.1-neo,rep1 (ChIP-seq)


title: HeLa cells,IRF7(input),linear pcDNA3.1-neo,rep2 (ChIP-seq)


title: GM12878, biol rep1, 0h ActD (pre-treatment)


title: roots, CK-OX-3-RNA-seq

value: OX


title: XX_D2_REPi_RE96_GFP-Low_R2


title: roots, CK-WT-2-RNA-seq


title: roots, CK-OX-2-RNA-seq


title: HeLa cells,IRF7(input),control,rep3 (ChIP-seq)


title: XX_D2_REPi_RE96_GFP-High_R2


title: HeLa cells,IRF7(input),control,rep2 (ChIP-seq)


title: roots, Al-WT-2-RNA-seq

value: Al


title: roots, Al-WT-3-RNA-seq


title: XX_D2_REPi_RE96_Unsorted_R2


title: roots, Al-WT-1-RNA-seq


title: roots, Al-OX-3-RNA-seq


title: HeLa cells,IRF7(input),control,rep1 (ChIP-seq)


title: XX_D2_REPi_RE96_GFP-Low_R1


title: roots, Al-OX-2-RNA-seq


title: XX_D2_REPi_RE96_Unsorted_R3


title: XX_D2_REPi_RE96_GFP-High_R1


title: roots, Al-OX-1-RNA-seq


title: HeLa cells,IRF7(IP),linear pcDNA3.1-neo,rep2 (ChIP-seq)

value: IRF-7 Antibody #4920


title: M10-OX3-R-4-RNA-seq

data_processing:
Illumina Casava software used for basecalling.
（1）Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted )（2）Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality).（3）Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%)
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
The GO （Gene Ontology, http://geneontology.org/）enrichment of DEGs was implemented by the hypergeometric test. GO terms with q<0.05 were considered to be significantly enriched.The KEGG PATHWAY enrichment of DEGs was implemented by the hypergeometric test. KEGG terms with q<0.05 were considered to be significantly enriched. genome build
Supplementary files format and content: tab-delimited text files include raw counts for each Sample .
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

value: Mn


title: M10-OX3-R-3-RNA-seq


title: HeLa cells,IRF7(IP),linear pcDNA3.1-neo,rep1 (ChIP-seq)


title: M10-OX3-R-2-RNA-seq


title: C-OX3-R-4-RNA-seq


title: XX_D2_REPi_RE95_GFP-Low_R3

value: 2iL-withdrawal/Pooled CRISPRi screen


title: roots, CK-OX-1-RNA-seq


title: XX_D2_REPi_RE96_Unsorted_R1


title: HeLa cells,IRF7(IP),control,rep3 (ChIP-seq)

value: HeLa


title: C-OX3-R-2-RNA-seq


title: XX_D2_REPi_RE95_GFP-High_R3


title: C-OX3-R-3-RNA-seq


title: HeLa cells,IRF7(IP),control,rep2 (ChIP-seq)

value: human cervical adenocarcinoma cell


title: M10-W-R-2-RNA-seq


title: M10-W-R-1-RNA-seq


title: HeLa cells,IRF7(IP),control,rep1 (ChIP-seq)


title: C-W-R-4-RNA-seq


title: XX_D2_REPi_RE95_Unsorted_R3


title: HeLa cells,IRF7(IP),linear pcDNA3.1-neo,rep3 (ChIP-seq)

value: transfected with linear pcDNA3.1-neo plasmid


title: C-W-R-3-RNA-seq


title: XX_D2_REPi_RE95_GFP-Low_R2

value: Embryonic stem cells


title: lung tissue-IPF-IPF9_r162.1

type: genomic

city: Hamilton

first: John

middle: Edward

last: McDonough

state: ON

address: 50 Charlton Ave E

country: Canada

institute: McMaster University

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
IDAT files were processed with R package minfi, preserving control probe data. Quality control steps were performed to exclude failed samples with low-quality reads as well as any probes that failed in one or more samples (i.e. detection p-value > 0.01, representing the probability that the signal differs from the background signal due to chance as estimated from negative controls). MethylToSNP was used to eliminate CpG probes at single nucleotide polymorphisms (SNPs), while reducing data loss by considering SNPs specific only to the studied participants, based on the similarity of site-specific methylation patterns to expected SNPs. Probes in the array that showed cross-reactivity were excluded using a list(3) and in total, 47,138 probes were removed, leaving 819,618 probes for further analysis. Data were normalized using the normal-exponential using out-of-band probes (Noob) normalization method, to account for technical variation in the background fluorescence signal, and through the Beta-mixture quantile normalization (BMIQ) method in package watermelon to adjust the beta-values of type-II design probes to the statistical characteristics of type-I probes. However, 𝞫-values have significant heteroscedasticity in the low and high methylation ranges and were therefore logit-transformed to M-values for statistical analysis for a more constant standard deviation across the methylation range.
processed value definition: Average beta

label: Cy5 and Cy3

source_name: lung tissue sample

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extract from lung tissue samples using Qiagen DNeasy DNA extraction kits.

tag: disease

value: IPF

tag: Stage

tag: subject

value: M

tag: age

value: lung tissue sample


title: XX_D2_REPi_RE95_GFP-High_R2

value: CAST / C57BL/6


title: XX_D2_TFiMini_Selected_R2

description:
TFiMini.count.txt
TFiMini.count_normalized.txt

data_processing:
*library strategy: Pooled CRISPR screen
Count tables were generated using MAGeCK (v0.5.9.3) with [mageck count –norm-method control](Li et al. 2014).
Screen targets were enriched using MAGeCK (v0.5.9.3) with the normalized count tables and [mageck mle --permutation-round 10](Li et al. 2014).
Assembly: mm10
Supplementary files format and content: Count tables (.txt)
Supplementary files format and content: Normalized count tables (.txt)
Supplementary files format and content: Enrichment using mageck mle (.txt)

growth_protocol: TX1072 SP107/SP427 mESCs were cultured on 0.1% gelatin-coated flasks in serum-containing medium supplemented with LIF (SL conditions) (DMEM (Sigma), 15% ESC-grade FBS (GIBCO), 0.1 mM b-mercaptoethanol, 1000 U/ml LIF (Millipore), 3 mM Gsk3 inhibitor CT-99021, 1 mM MEK inhibitor PD0325901 (Axon)). The cells were cultured at a density of 4*104 cells/cm2 and passaged every second day.

extract_protocol:
Following cell sorting at the FACS, genomic DNA was isolated using phenol/chloroform extraction. First, cell pellets were incubated for 14 hours at 65 °C in de-crosslinking buffer (1% SDS (Invitrogen), 1.25 µl DTT (Roth) and 10 µl 5M NaCl (Sigma) in Tris-EDTA buffer (Sigma)). Next, 20 µl RNAse A (10 mg/ml, New England Biolabs) were added and the solution incubated for 1 hour at 37 °C. Following, 5 µl Proteinase K (20 mg/ml, Ambion) was added and the solution incubated for 1 hour at 50 °C. Subsequently, 275 µl of Phenol/Chloroform (Roth) were added and the mixture vortexed for 1 min. The samples were then centrifuged for 10 min at 13,000 rpm. The aqueous phase, containing the genomic DNA, was transferred to a new tube and the sample was cleaned using ethanol precipitation. The pellets were dried and resuspended in 50 µl water.
The guide cassette was amplified for 20 cycles using the KAPA HiFi PCR ReadyMix with primers OG115/OG116.  To keep 300x coverage, at least 20 µg (TFi screen) or 1.6 µg (TFiMini screen) of genomic DNA were amplified per sample. Following clean-up with the DNA Clean & Concentrator Kit, sequencing barcodes were added in a second PCR using the KAPA HiFi PCR ReadyMix for 11-12 cycles

treatment_protocol: A coverage of >300x was retained during all steps. Following transduction of the TFi Lib into the TX SP107 cell line under SL conditions, the cells were selected for three days using puromycin. Subsequently, the cells were transferred into 2iSL medium. At the same time, 1*10^7 cells were frozen (Selected population).  After three days, the split dCas9-KRAB system was induced via the addition of ABA. The cells were then differentiated for 48 hours via 2i/LIF-withdrawal. During the FlowFISH staining for Xist RNA, 1*10^7 cells were frozen (Unsorted population). Using flow cytometry, cells were according to Xist expression into Xist-high (top 15%), Xist-low (bottom 15% of the Xist-positive cells) and Xist-neg (bottom 15%) populations. At least 1.5*10^7 cells were recovered per population.   For the TFiMini screen, the TX SP427 cell line was transduced under SL conditions in the presence of dTAG-13. Following three days of puromycin selection, the cells were transferred to 2iSL conditions. At the same time, 1*10^7 cells were frozen (Selected population). After 8 days, the CasTuner system was induced via the removal of dTAG-13 from the medium. Two days later, the cells were differentiated via 2i/LIF-withdrawal. At the same time, 1*10^7  cells were frozen (2iSL population). After two days of 2i/LIF-withdrawal, the cells were stained via FlowFISH and sorted according to Xist expression into Xist-High (top 15%) and Xist-Neg (bottom 15%) populations using flow cytometry. At least 5*10^5 cells were recovered per population.


title: C-W-R-2-RNA-seq


title: lung tissue-IPF-IPF8_r147.3


title: XX_D2_TFiMini_2iSL_R2


title: XX_D2_REPi_RE95_Unsorted_R2


title: XX_D2_TFiMini_Negative_R2

description:
TFiMini.count.txt
TFiMini.count_normalized.txt
TFiMini_mle_HighvsNeg.txt


title: XX_D2_REPi_RE95_GFP-Low_R1


title: XX_D2_TFiMini_2iSL_R1


title: XX_D2_TFiMini_Selected_R1


title: M10-W-R-3-RNA-seq


title: lung tissue-IPF-IPF1_r3.16


title: XX_D2_REPi_RE95_GFP-High_R1


title: XX_D2_TFiMini_Negative_R1


title: XX_D2_TFiMini_High_R1


title: XX_D2_REPi_RE95_Unsorted_R1


title: lung tissue-CONTROL-CTRL8_r6989.1109

value: CONTROL


title: Alveolar macrophage, wcl stimulation, after vaccine, Rep2

first: Zhou

last: Xing

state: Ontario

address: MDCL building, 1280 Main St W

department: Division of Respirology

description:
Library name: wcl_3_45
Column name in processessed file: wcl_3_45

data_processing:
Raw sequence data were exported to FASTQ format and were filtered based on quality scores.
Next the reads were mapped to  the UCSC/HG38 reference version using HISAT2.
The counts were obtained by using ht-seq count with the “intersection-strict” option.
Counts were transformed with TMM transformation and then normalized with VOOM.
Assembly: hg38
Supplementary files format and content: Processed data CSV file contains a matrix containing data from all samples.

source_name: Lung

growth_protocol: Not available

extract_protocol:
Total RNA is extracted using RNeasy Plus Kit from Qiagen which includes gDNA eliator columns, following the manufacturer's protocol.
RNA QC was performed using the Agilent 4200 TapeStation RNA ScreenTape. mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module with 200 ng of total RNA input. Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep kit and Multiplex Oligos for Illumina (Unique Dual Index Primer Pairs Set 3). Library QC was performed using the Agilent 4200 TapeStation D1000 ScreenTape to assess fragment sizes and using qPCR to determine the functional library concentration. Libraries were normalized, pooled, and QC checks were repeated on the final library pool prior to sequencing.

treatment_protocol: Revived bronchoalvaeolar cells were enriched for alveolar macrophages by removal of non-ahherent cells via extensive wasjing with PBS and then cultured with or without whole cell lysated of Mycobacerium tuberculosis stimulant for 16 hours in complete RPMI supplemented with 2%fetal bovine serum.

value: Lung

value: Alveolar macrophage

value: Not available

value: Stimulated


title: XX_D2_REPi_RE93_GFP-Low_R3


title: Alveolar macrophage, wcl stimulation, after vaccine, Rep1

description:
Library name: wcl_3_41
Column name in processessed file: wcl_3_41


title: Alveolar macrophage, wcl stimulation, after vaccine, Rep3

description:
Library name: wcl_3_46
Column name in processessed file: wcl_3_46


title: XX_D2_REPi_RE93_GFP-High_R3


title: lung tissue-IPF-IPF3_r25.59


title: Alveolar macrophage, wcl stimulation, before vaccine, Rep2

description:
Library name: wcl_1_45
Column name in processessed file: wcl_1_45


title: lung tissue-IPF-IPF5_r110.30


title: Alveolar macrophage, wcl stimulation, before vaccine, Rep1

description:
Library name: wcl_1_41
Column name in processessed file: wcl_1_41


title: XX_D2_REPi_RE93_Unsorted_R3


title: Alveolar macrophage, wcl stimulation, before vaccine, Rep3

description:
Library name: wcl_1_46
Column name in processessed file: wcl_1_46


title: lung tissue-IPF-IPF7_r127.8


title: lung tissue-IPF-IPF2_r11.25


title: Alveolar macrophage, no stimulation,after vaccine, Rep3

description:
Library name: unstim_3_46
Column name in processessed file: unstim_3_46


title: Alveolar macrophage, no stimulation,after vaccine, Rep2

description:
Library name: unstim_3_45
Column name in processessed file: unstim_3_45


title: XX_D2_REPi_RE93_GFP-Low_R2

description:
REPi.count.txt
REPi.count_normalized.txt
REPi_interaction_scores.txt


title: XX_D2_TFiMini_High_R2


title: lung tissue-CONTROL-CTRL4_r146.84


title: Alveolar macrophage, no stimulation,after vaccine, Rep1

description:
Library name: unstim_3_41
Column name in processessed file: unstim_3_41


title: XX_D2_REPi_RE93_GFP-High_R2


title: Alveolar macrophage, no stimulation, before vaccine, Rep2

description:
Library name: unstim_1_45
Column name in processessed file: unstim_1_45


title: lung tissue-CONTROL-CTRL1_r62.148


title: Alveolar macrophage, no stimulation, before vaccine, Rep3

description:
Library name: unstim_1_46
Column name in processessed file: unstim_1_46


title: XX_D2_REPi_RE93_Unsorted_R2


title: Alveolar macrophage, no stimulation, before vaccine, Rep1

description:
Library name: unstim_1_41
Column name in processessed file: unstim_1_41


title: bone marrow, ex vivo, memory T cells, d3, GEX, TCR, CITE-seq.

first: Frederik

middle: Richard

last: Heinrich

address: Chariteplatz 1

department: Bioinformatics

description: 10X Genomics

data_processing:
Demultiplexing, barcode processing, and gene quantification was performed using Cell Ranger Single Cell Software Suite 5.0.0 with refdata-gex-GRCh38-2020-A as reference and expected-cells number of 3000 for each sample; polymorphisms removed. Raw sequence reads from the TCR libraries were processed using the cellranger’s vdj pipeline in default parameter settings with refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0 as reference and merged without size normalization with cellranger’s count. as reference.
Assembly: GRCh38
Supplementary files format and content: .h5 and .csv
Library strategy: scRNAseq, CITE-seq

source_name: bone marrow

extract_protocol:
Memory T cells were isolated from fresh ex-vivo paired blood and bone marrow samples of three different donors with straight from blood magnetic enrichment (Miltenyi Biotech) Followed by cell sorting trough flow cytometric analysis.
Chromium Next GEM Single Cell 5’ reagent kits v2 (dual index) with featured barcode technology for cell surface protein (CITE) mapping (10X Genomics) were used as stated in the manufacturer’s protocol. Final CITE-Seq libraries were generated after index PCR with dual Index Kit TN Set A (10X Genomics) while final GEX and TCR libraries were generated after fragmentation, adapter ligation and final index PCR with a dual Index Kit TT Set A (10X Genomics). Libraries were quantified using a Qubit HS DNA assay kit (LifeTechnologies) and fragment sizes were determined using a HS NGS Fragment (1-6000 bp) kit (Agilent).All libraries (GEX and CITE and TCR libraries) were sequenced on a NextSeq2000 sequencer (Illumina) using a P3 reagent kit (100 cycles) (Illumina) and following the sequencing conditions recommended by 10x Genomics: read1: 26 nt, read2: 90 nt, index1: 10 nt, index2: 10 nt.(35)

treatment_protocol: Ex vivo blood and bonbe marrow were washed with Actinomycin D buffer during T cell isolation

value: bone marrow

value: memory T cells

value: actinomycin D


title: lung tissue-IPF-IPF8_r147.48


title: bone marrow, ex vivo, memory T cells, d2, GEX, TCR, CITE-seq.

description: 10X Genomics


title: XX_D2_REPi_RE93_GFP-Low_R1

value: 2iL-withdrawal/Pooled CRISPRi screen


title: blood, ex vivo, memory T cells, d3, GEX, TCR, CITE-seq.

description: 10X Genomics

source_name: blood

value: blood


title: blood, ex vivo, memory T cells, d2,GEX, TCR, CITE-seq.

description: 10X Genomics


title: lung tissue-CONTROL-CTRL7_r6983.404


title: XX_D2_REPi_RE93_GFP-High_R1


title: XX_D2_REPi_RE93_Unsorted_R1


title: bone marrow, ex vivo, memory T cells, d1, GEX, TCR, CITE-seq.

description: 10X Genomics


title: lung tissue-CONTROL-CTRL2_r94.3


title: lung tissue-CONTROL-CTRL4_r146.116


title: XX_D2_REPi_RE85_GFP-Low_R3


title: lung tissue-IPF-IPF10_r190.23


title: bone marrow, ex vivo, memory T cells, d1, GEX, TCR, CITE-seq

description: 10X Genomics

data_processing:
Demultiplexing, barcode processing, and gene quantification was performed using Cell Ranger Single Cell Software Suite 5.0.0 with refdata-gex-GRCh38-2020-A as reference and expected-cells number of 3000 for each sample; polymorphisms removed. Raw sequence reads from the TCR libraries were processed using the cellranger’s vdj pipeline in default parameter settings with refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0 as reference and merged without size normalization with cellranger’s count. as reference.
Assembly: GRCh38
Supplementary files format and content: .fasta and .csv
Library strategy: scRNA TCR


title: bone marrow, ex vivo, memory T cells, d2, GEX, TCR, CITE-seq

description: 10X Genomics


title: blood, ex vivo, memory T cells, d3, GEX, TCR, CITE-seq

description: 10X Genomics


title: lung tissue-IPF-IPF7_r127.28


title: lung tissue-IPF-IPF9_r162.4


title: blood, ex vivo, memory T cells, d2,GEX, TCR, CITE-seq

description: 10X Genomics


title: XX_D2_REPi_RE85_GFP-High_R3


title: blood, ex vivo, memory T cells, d1, GEX, TCR, CITE-seq

description: 10X Genomics


title: XX_D2_REPi_RE85_Unsorted_R3


title: lung tissue-IPF-IPF1_r3.68


title: VCaP_scRNA_DexDHT

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software 7.0.0.
Downstream analyses (UMAP, dotplots) were performed with Seurat software.
Assembly: hg38
Supplementary files format and content: Raw barcodes and matrix from Cell Ranger
Supplementary files format and content: Filtered barcodes, features, and matrix from Cell Ranger

source_name: VCaP

growth_protocol: VCaP cells were grown in DMEM medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin and 1 µg/ml streptomycin. All cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
Single cell suspensions were harvested and washed according to published protocol (10x Genomics, #CG00054). Isolated cells were concentrated to 700 cells per µl.
scRNA-seq libraries were prepared with Single Cell 3' Kit v3.1 according to published protocol (10x Genomics, #CG000315). Target cell recovery was set at 2000 cells.

treatment_protocol: VCaP cells were treated with vehicle (EtOH) or 100 nM of Dexamethasone (Dex) or 100 nM of dihydrotestosterone (DHT) or Dex and DHT for 18 h before the start of single cell suspension extraction.

value: VCaP

value: Vertebral Cancer of the Prostate

tag: dex treatment

tag: dht treatment


title: VCaP_scRNA_DHT

description: 10x Genomics


title: VCaP_scRNA_Dex

description: 10x Genomics


title: VCaP_scRNA_EtOH

description: 10x Genomics


title: blood, ex vivo, memory T cells, d1, GEX, TCR, CITE-seq.

description: 10X Genomics


title: bone marrow, ex vivo, memory T cells, d3, GEX, TCR, CITE-seq

description: 10X Genomics


title: lung tissue-CONTROL-CTRL8_r6989.1149


title: XX_D2_REPi_RE85_GFP-Low_R2

value: Embryonic stem cells


title: lung tissue-IPF-IPF4_r50.27

value: IPF


title: lung tissue-IPF-IPF2_r11.18

value: M


title: XX_D2_REPi_RE85_Unsorted_R2


title: XX_D2_REPi_RE85_GFP-Low_R1


title: lung tissue-IPF-IPF5_r110.23

value: lung tissue sample


title: lung tissue-CONTROL-CTRL2_r94.137


title: lung tissue-CONTROL-CTRL1_r62.50


title: XX_D2_REPi_RE85_Unsorted_R1

value: CAST / C57BL/6


title: lung tissue-CONTROL-CTRL7_r6983.791

value: CONTROL


title: XX_D2_REPi_RE61_GFP-Low_R3


title: XX_D2_REPi_RE85_GFP-High_R2


title: XX_D2_REPi_RE61_GFP-High_R3


title: D9-Poliprotect (F) + pH1-3

type: RNA

city: Sansepolcro

first: Jacopo

last: Lucci

state: Arezzo

address: Loc. Aboca, 20

country: Italy

institute: Bios-Therapy, Physiological Systems For Health S.p.A

description: treated with Poliprotect (F) 310 mg/ml (3,2µl) +HBSS pH1 (26,8µl) + HBSS pH7.4 (600µl)

hyb_protocol: Fragmented and labeled cDNA was prepared according to the manufacturer's instructions and hybridized to a Human Clariom S 24-array plate for 17 h at 45°C on a GeneTitan MC Instrument (Applied Biosystems, ThermoFisher Scientific). Arrays were washed and stained on a GeneTitan MC Instrument (Applied Biosystems, ThermoFisher Scientific).

scan_protocol: Arrays were scanned using the GeneTitan MC Instrument (Applied Biosystems, ThermoFisher Scientific). Affymetrix GeneChip Command Console Software (AGCC, ThermoFisher Scientific) was used for GeneTitan MC Instrument control.

data_processing: Data analysis were performed using Transcriptomic Analysis Console Software (TAC, ThermoFisher Scientific) that provides quality control analysis, performs normalization and summarization that provides a list of differentially expressed genes based on the limma package approach (Bioconductor), using a threshold of p-value ≤0.05) from the biological triplicates of each condition.

label: biotin

source_name: NCI-N87 treated with Poliprotect (F) + pH1 (apical ) + HBSS pH7.4 (basolateral)

label_protocol: Biotinylated cRNA was prepared according to the standard ThermoFisher Scientific protocol from 6 ug total RNA (GeneChip™ 3’ IVT Pico Kit Manual Workflow).

growth_protocol: NCI-N87 cells were seeded on 24 well-plate polyester membrane inserts and treated 8 days post-seeding.

extract_protocol: Total RNA was extracted from cells lysates using an QIAsymphony RNA Kit (Qiagen,) with the QIAsymphony SP instrument (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Apical treatmet: NCI-N87 were first pre-incubated for 1h into in incubator, shaking (80 rpm) in HBSS pH7.4. In this phase, HBSS was provided to both the apical and basolateral sides. The basolateral HBSS was then replaced with 600µl of fresh HBSS pH7.4 and apical HBSS was then replaced by treatment solutions as follows:  -Acid-induced damage: the apical HBSS was replaced by 27 µl of HBSS acidified to pH1 with HCl and incubation continued in the incubator with shaking for 30 min.   -Poliprotect (F) : the apical HBSS was removed and cells were treated with 3µl of the product dissolved in HBSS pH1 at 310 mg/ml concentration. An additional 27µl of HBSS pH1 was layered on top of the thus-formed barrier to represent the presence of the acidic stress. The incubation continued in the incubator, shaking for 30 minutes.  -control: the apical HBSS was replaced by 27µl of fresh HBSS pH7.4 and incubation continued in the incubator with shacking for 30 min.   Basolateral treatment: After pre-incubation of 1h in incubator (37°, 5% CO2), shaking (80 rpm) in HBSS pH7.4, treatments were performed as follows:  -Acid-induced damage: the apical and basolateral HBSS pH7.4 was replaced by HBSS pH1 (27µl) and culture medium RPMI-1640 (600µl) respectively. Incubation continued in the incubator with shaking for 30 min.   -Poliprotect (F): the apical and basolateral HBSS pH7.4 was replaced by HBSS pH1 (27µl) and by Poliprotect (F) solution (600µl) at a concentration of 110 µg/ml in RPMI-1640 respectively. The solution of the Poliprotect (F) was prepared by diluting in RPMI-1640 the solution used for the apical treatment (310 mg/ml), and incubation continued in the incubator with shaking for 30 min.  -control: the apical HBSS pH7.4 was replaced by 27µl of fresh HBSS pH7.4, the basolateral HBSS pH7.4 was replaced by 600µl of RPMI-1640 and incubation continued in the incubator with shacking for 30 min.

value: gastric cell line

tag: features

value: Immortalized gastric cell line terminally differentiated

value: adult


title: XX_D2_REPi_RE61_Unsorted_R3


title: XX_D2_REPi_RE85_GFP-High_R1


title: F7-Poliprotect (F)-2

description: treated with Poliprotect (F) 110 µg/ml in RPMI-1640 medium (600µl) + HBSS pH1(26,8µl)

source_name: NCI-N87 treated with Poliprotect (F) (basolateral )+ HBSS pH1 (apical)


title: E7-pH1 (basolateral)-2

description: treated with HBSS pH1(26,8µl)+ RPMI-1640 medium (600µl)

source_name: NCI-N87 treated with HBSS pH1 (apical )+ RPMI-1640 (basolateral)


title: lung tissue-IPF-IPF7_r127.37

tag: Sex


title: D5-Poliprotect (F) + pH1-1


title: E5-pH1 (basolateral)-1


title: D7-Poliprotect (F) + pH1-2


title: E9-pH1 (basolateral)-3


title: F5-Poliprotect (F)-1


title: C9-pH1 (apical)-3

description: treated with HBSS pH1(26,8µl)+ HBSS pH7.4 (600µl)

source_name: NCI-N87  treated with HBSS pH1 (apical )+HBSS pH7.4 (basolateral)


title: F9-Poliprotect (F)-3


title: lung tissue-CONTROL-CTRL4_r146.100

tag: tissue


title: XX_D2_REPi_RE61_GFP-High_R2


title: D9-pH7.4 (basolateral)-3

description: treated with HBSS pH7.4 (26,8µl) + RPMI-1640 medium (600µl)

source_name: NCI-N87 treated with HBSS pH7.4 (apical )+ RPMI-1640 (basolateral)


title: C7-pH1 (apical)-2


title: D7-pH7.4 (basolateral)-2


title: 4-2537

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description: Library name: TCCTGAGC

data_processing:
The raw sequences from all the samples were aligned to the GRCm38/GRCh38 reference genome and quantified using Drop-Seq pipeline.
Assembly: GRCm38/GRCh38 reference genome
Supplementary files format and content: h5 files of the Count matrix of these sequencing runs.

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Briefly, frozen tissue was minced with a razor blade and mechanically homogenized in Nuclei EZ Lysis Buffer (Sigma-Aldrich). After incubation for 5 min, the homogenate was filtered through a 70µm strainer mesh. Two washing steps were performed with a 1% solution of bovine serum albumin (BSA) (Sigma-Aldrich, A3294-100G) in phosphate buffered saline (PBS) (Thermo Fisher Scientific, 14190250), with addition of 0.2U/µL of RNase Inhibitor (Lucigen, 30281-2). Centrifugation occurred at 500xg for 5 minutes at 4°C. To separate nuclei from cell debris, nuclei suspensions were incubated for 10 min with 10µg/mL 4',6-Diamidin-2-phenylindol (DAPI) (Sigma, #D9542) in wash buffer to stain DNA. Subsequently, DAPI+ nuclei were sorted via fluorescence activated cell sorting (FACS) and utilized for Drop-Seq as described below. When Aldh1l1Cre-ERT2/TdTomato astrocyte reporter mice (The Jackson Laboratory, #031008 and #007909) were used, 200mg/kg Tamoxifen (Sigma-Aldrich, T5648) diluted in corn oil (Sigma-Aldrich, C8267) was administered intraperitoneally 2-4 weeks before starting the experiment and TdTomato induction was confirmed by flow cytometry at the time of measurement. 1 x 105 GL261-Luc2 cells (ATCC) were implanted intracranially. GL261 cells with passage number < 10 were detached using Accutase (Stemcell Technologies) and cell suspensions prepared in serum-free DMEM. The surgical procedure was performed following IACUC guidelines for survival surgery. Briefly, a small animal stereotaxic frame (David Kopf Instruments) was placed within a laminar flow cabinet and a sterile field containing all surgical instruments and tools was established. An activated charcoal filter (VetEquip) was connected to the outflow to adsorb Isoflurane. Mice were individually placed in an anesthesia induction chamber and a flow of Isoflurane (Patterson Veterinary) at 2.5-3 L/h mixed with oxygen at 2.5 L/h was initiated. The top of the skull was shaved and disinfected using isopropyl swabs (Becton Dickinson) and application of the antiseptic Betadine (Purdue Products). For intracranial injection, the mouse skull was fixed on the stereotaxic frame using ear bars and a mouthpiece for incisor fixation and gas supplementation. Sufficient depth of anesthesia was confirmed by a toe pinch, and mouse vital signs were monitored throughout the procedure. Following a 2cm incision on the scalp, the injection coordinates were determined from bregma. A hole was drilled at the +1.8 mm (lateral) and +0.5 mm (anterior) position. A 25µl glass syringe (Hamilton) was inserted until -3.5 mm depth and slowly retracted 0.5 mm to the final injection site at -3mm depth. 3µL of GL261 cell suspension were gradually injected at a rate of 1 µl/ min. Control mice received a sham injection of 3µL DMEM. Astrocyte sorting from Aldh1l1Cre-ERT2/TdTomato astrocyte reporter mice was performed by gating Live+ CD45- CD11b- TdTomato+. Drop-Seq113 was used for scRNA-seq via co-encapsulation of uniquely barcoded beads and single cells in nanoliter droplets prior to cell/nucleus lysis and transcriptome capture. Following the protocol developed by Macosko et al.113, barcoded MACOSKO-2011-10 B beads (Chemgenes) linked to 108 uniquely barcoded oligonucleotides (5’-Bead–Linker-TTTTTTTAAGCAGTGGTATCAACGCAGAGTACJJJJJJJJJJJJNNNNNNNNTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-3’) were resuspended in a wash solution made of 10 mM Tris pH 8.0 (Sigma-Aldrich, T3038), 1 mM EDTA (Amresco, E177-100ML) and 0.01% Tween‐20 (Sigma-Aldrich, P9416) (TE-TW) at a density of 3 x 105/mL and stored at 4°C. Immediately prior to use, beads were centrifuged at 1000xg and resuspended in 1mL of lysis buffer composed of 570µL OptiPrep (Sigma-Aldrich, D1556-250ML), 120µL 20% Ficoll PM‐400 (Cytiva, 17-0300-10), 20µL 10% Sarkosyl (Sigma-Aldrich, L7414-50ML), 40µL 0.5M EDTA (Amresco, E177-100ML), 200µL 1M Trizma hydrochloride solution pH 8.0 (Sigma-Aldrich, T2663-1L), 50µL 1M dithiothreitol (Thermo Fisher Scientific, P2325) (DTT). Sorted cells or nuclei were taken up in 16% OptiPrep at a concentration of 2.5x105/mL in 1mL. If fewer cells or nuclei were available, Fluorinert FC-40 (Sigma Aldrich, F9755-250ML) was used as a backflow liquid. If fewer than 1x105 cells were available, bead concentrations were doubled to 6x105/mL to increase the capture rate, which follows a Poisson distribution. Beads and cells were taken up in a 3mL syringe (BD), adding a magnetic disk (VP Scientific, 772DP-N42-5-2) and using a magnetic stirrer (VP Scientific) to homogenize bead suspensions. QX200 Droplet Generation Oil for EvaGreen (BioRad, 1864006) was taken up in a 10mL syringe (BD). Three Legato 100 syringe pumps (KD Scientific) were loaded with oil, cell, and bead syringes, and PE/2 polyethylene microtubing (Scientific Commodities Inc., BB31695-PE/2) was used to connect them to the device input holes of PDMS devices placed on an inverted light microscope with an attached Fire-i 830b camera (Unibrain). Fire-i (Unibrain) was used to visualize rapidly flowing droplets with lowest shutter speed and highest exposure and gain settings. The device was initially primed with oil, prior to connecting cell and lastly bead flows at flow rates of 4500, 1500 and 1500 µL/h, respectively. Output flow containing droplets was collected for 20-25min or until the cell suspension was used up. For droplet breakage, approximately 1/3 of excess oil volume was added as 97% 1H,1H,2H,2H-Perfluoro-1-octanol (Sigma-Aldrich, 370533), along with 30mL of 6X sodium chloride-sodium citrate (SSC) buffer (National Diagnostics, EC-873). Emulsions were shaken a few times and centrifuged at 1000xg for 1min, resulting in a visible bead layer floating at the interface of oil and SSC. In the following steps, as much of the oil and SSC as possible was removed, while topping up with fresh SSC and centrifuging to wash the beads prior to reverse transcription (RT) into cDNA. Beads were washed in 300µL of 1x RT buffer (Thermo Fisher Scientific, EP0742) prior to incubation in 200µL RT mix composed of 75µL H2O, 40µL 5x RT buffer, 40µL 20% Ficoll PM-400 (Cytiva, 17-0300-10), 20µL 1mM dNTPs (Thermo Fisher Scientific, R0194), 5µL RNase Inhibitor (Lucigen, 30281-2), 10µL 50µM Template Switch Oligo (AAGCAGTGGTATCAACGCAGAGTGAATrGrGrG, IDT) and 10µL (with 2000U) Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific, EP0742) for 30 min at room temperature and 90 min at 42°C (with rotation in both cases). Reaction mixtures were then washed with 1mL of a solution containing 10mM Tris pH 8.0, 1mM EDTA and 0.5% sodium dodecyl sulfate (Sigma-Aldrich, L3771-100G) (TE-SDS), twice with 1mL of TE-TW, and once with 1mL 10mM Tris pH 8.0. To remove bead-linked oligonucleotides that had not captured an mRNA molecule, beads were incubated in a mix of 20µL 10x Exonuclease I buffer (Thermo Fisher Scientific, EN0581), 170µL H2O and 10µL (with 200U) Exonuclease I (Thermo Fisher Scientific, EN0581) for 45min at 37°C with rotation. After washing once with TE-SDS, twice with TE-TW and once with 1mL H2O beads were counted using a hemocytometer chamber and divided into 4000 beads per aliquot in PCR tubes. A PCR mix containing 24.6µL H2O, 0.4µL 100µM SMART PCR primer (AAGCAGTGGTATCAACGCAGAGT) (IDT) and 25µL 2x Kapa HiFi Hotstart Readymix (Kapa Biosystems, 7958927001) were added. PCR was performed in a thermocycler with the following program to amplify cDNA molecules: 95°C (3 min); 4 cycles of: 98°C (20 s), 65°C (45 s), 72°C (3 min); 9 cycles of: 98°C (20 s), 67°C (20 s), 72°C (3 min); 72°C (5 min); 4°C hold. PCR products were purified using AMPure XP beads (Beckman Coulter, A63881) at a 0.6x ratio according to manufacturer's protocol, eluting all samples in 50µL molecular grade H2O (Thermo Fisher Scientific, AM9937). At this point, the distribution of fragment sizes within cDNA libraries was quantified using a 2100 Bioanalyzer (Agilent) instrument with High Sensitivity DNA Kit (Agilent, 5067-4626). Library concentration and quality was assessed by a rounded curve with average sizes around 700 bp. In cases where DNA concentration was not sufficient, additional PCR cycles with the following conditions were added as needed: 98°C (20 s), 67°C (20 s), 72°C (3 min). 600pg of cDNA library in 5µL were used for fragmentation and addition of sample tags by means of the Nextera XT DNA Library Prep Kit (Illumina, FC-131-1096). cDNA was added to 10µL of Nextera Tagment DNA buffer and 5µL of Amplicon Tagment Mix. After incubation for 5min at 55°C, 5µL of Neutralize Tagment buffer was added. After 5 min at room temperature, a mix containing 15µL Nextera PCR Mix, 8µL H2O, 1µL 10µM New-P5-SMART PCR hybrid oligo (AATGATACGGCGACCACCGAGATCTACACGCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGT*A*C) (IDT), and 1µL of a 10µM sample-specific Nextera indexing oligonucleotide (Illumina, FC-121-1011). Samples underwent PCR with the following program: 95°C (30 s); 12 cycles of: 95°C (10 s), 55°C (30 s), 72°C (30 s); 72°C (5 min); 4°C hold. cDNA was purified AMPure XP beads at a 0.6x ratio and eluted in 10µL H2O. Library distribution was analyzed using a 2100 Bioanalyzer and the molarity-weighted average fragment size was calculated. The Library Quantification Kit (Kapa Biosystems) was used to determine library concentrations by qPCR according to standard protocol. Finally, 4µL samples were pooled at an equimolar ratio of 5nM. Finally, samples were sequenced using NovaSeq S2 at with a Custom Read 1 primer (GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC), estimating around 25,000 reads per STAMP. STAMPs were estimated by multiplying the cell number used (determined by flow rate, run time and concentration) with the co-encapsulation probability (given by the product of the encapsulation probability of either cells or beads). The co-encapsulation probability of single units follows a Poisson distribution as a function of droplet volume and cell or bead concentration and was 2.5% for mouse samples and on average 1.4% for human nuclei.
Library was constructed using Drop-Seq protocols

value: Brain


title: 6-6626

description: Library name: TAGGCATG


title: lung tissue-IPF-IPF10_r190.36


title: B7-pH7.4 (apical)-2

description: treated with HBSS pH7.4 (26,8µl) + HBSS pH7.4 (600µl)

source_name: NCI-N87 treated with HBSS pH7.4 (apical) + HBSS pH7.4 (basolateral)


title: B5-pH7.4 (apical)-1


title: XX_D2_REPi_RE61_Unsorted_R2


title: D5-pH7.4 (basolateral)-1


title: 12-8326

description: Library name: GTAGAGGA


title: lung tissue-IPF-IPF8_r147.43


title: XX_D2_REPi_RE61_GFP-Low_R2


title: 13-9287

description: Library name: GCTCATGA


title: C5-pH1 (apical)-1


title: B9-pH7.4 (apical)-3


title: lung tissue-IPF-IPF9_r162.11


title: XX_D2_REPi_RE61_GFP-Low_R1


title: 9-87584

description: Library name: GCTACGCT


title: 7-9225

description: Library name: CTCTCTAC


title: XX_D2_REPi_RE61_GFP-High_R1


title: 10-5102

description: Library name: CGAGGCTG


title: lung tissue-IPF-IPF10_r190.64


title: 8-6490

description: Library name: CAGAGAGG


title: lung tissue-IPF-IPF1_r3.45


title: 3-1174

description: Library name: AGGCAGAA


title: 11-8594

description: Library name: AAGAGGCA


title: lung tissue-CONTROL-CTRL5_r6978.537


title: PegN, D06, ENR, Rep3

city: Lausanne

first: Antonius

last: Chrisnandy

state: Vaud

address: Route Cantonale

department: SV

country: Switzerland

institute: EPFL

description: Library name: PegN, D06, ENR, Rep3

data_processing:
Reads were aligned to the mouse genome (GRCm39) using star (v.2.7.0e)
R was used to perform the differential expression analyses. Count values were imported and processed using edgeR.
Assembly: GRCm39
Supplementary files format and content: Text file includes raw counts for each Sample

source_name: Small intestine

growth_protocol: Murine intestinal epithelial organoids were maintained within a 3D hydrogel.

extract_protocol:
RNA was collected using RNeasy Micro Kit (Qiagen). For each condition 175 ng of total RNA was used for the construction of sequencing library.
Library was prepared using QuantSeq 3′ mRNA-Seq library preparation kit (Lexogen)

treatment_protocol: A single epithelial cell was cultured within different hydrogels: Matrigel, PEG supplemented with Laminin-1 and PEG only. Different culture media were used to control differentiation and stem cell maintenance.

value: Small intestine

value: Small intestinal organoid

value: WT

value: PegN  ENR

tag: time


title: XX_D2_REPi_RE58_GFP-Low_R3

source_name: Embryonic stem cells

tag: cell type

value: 2iL-withdrawal/Pooled CRISPRi screen


title: PegN, D06, ENR, Rep2

description: Library name: PegN, D06, ENR, Rep2

tag: genotype


title: XX_D2_REPi_RE58_GFP-High_R3

tag: treatment


title: lung tissue-IPF-IPF4_r50.46a


title: XX_D2_REPi_RE58_Unsorted_R3

tag: cell line


title: PegN, D06, ENRD, Rep2

description: Library name: PegN, D06, ENRD, Rep2

value: PegN  ENRD


title: lung tissue-IPF-IPF6_r120.110


title: lung tissue-CONTROL-CTRL8_r6989.1971


title: XX_D2_REPi_RE58_GFP-Low_R2


title: PegN, D06, ENRD, Rep1

description: Library name: PegN, D06, ENRD, Rep1


title: PegN, D06, ENRCV, Rep2

description: Library name: PegN, D06, ENRCV, Rep2

value: PegN  ENRCV


title: PegN, D06, ENRCV, Rep1

description: Library name: PegN, D06, ENRCV, Rep1


title: XX_D2_REPi_RE61_Unsorted_R1

value: Embryonic stem cells


title: XX_D2_REPi_RE58_GFP-High_R2


title: lung tissue-CONTROL-CTRL7_r6983.2284


title: PegN, D06, ENRCD, Rep3

description: Library name: PegN, D06, ENRCD, Rep3

value: PegN  ENRCD


title: lung tissue-CONTROL-CTRL8_r6989.1814

value: M


title: lung tissue-CONTROL-CTRL7_r6983.405

value: lung tissue sample


title: XX_D2_REPi_RE58_Unsorted_R2

value: CAST / C57BL/6


title: PegN, D04, ENRCV, Rep3

description: Library name: PegN, D04, ENRCV, Rep3


title: XX_D2_REPi_RE58_GFP-Low_R1


title: lung tissue-IPF-IPF1_r3.76

value: IPF


title: PegN, D04, ENRCV, Rep2

description: Library name: PegN, D04, ENRCV, Rep2


title: PegN, D04, ENRCV, Rep1

description: Library name: PegN, D04, ENRCV, Rep1


title: PegN, D06, ENR, Rep1

description: Library name: PegN, D06, ENR, Rep1


title: PegN, D06, ENRCD, Rep2

description: Library name: PegN, D06, ENRCD, Rep2


title: lung tissue-IPF-IPF10_r190.24


title: XX_D2_REPi_RE58_Unsorted_R1


title: XX_D2_REPi_RE58_GFP-High_R1


title: PegLam, D06, ENR, Rep3

description: Library name: PegLam, D06, ENR, Rep3

value: PegLam  ENR


title: lung tissue-IPF-IPF9_r162.12


title: PegN, D06, ENRCD, Rep1

description: Library name: PegN, D06, ENRCD, Rep1


title: PegLam, D06, ENR, Rep2

description: Library name: PegLam, D06, ENR, Rep2


title: PegLam, D06, ENR, Rep1

description: Library name: PegLam, D06, ENR, Rep1


title: lung tissue-IPF-IPF8_r147.10


title: PegLam, D06, ENRD, Rep3

description: Library name: PegLam, D06, ENRD, Rep3

value: PegLam  ENRD


title: PegLam, D06, ENRD, Rep1

description: Library name: PegLam, D06, ENRD, Rep1


title: XX_D2_REPi_RE57R_GFP-High_R3


title: PegN, D06, ENRCV, Rep3

description: Library name: PegN, D06, ENRCV, Rep3


title: PegLam, D06, ENRD, Rep2

description: Library name: PegLam, D06, ENRD, Rep2


title: XX_D2_REPi_RE57R_GFP-Low_R3


title: PegLam, D06, ENRCV, Rep3

description: Library name: PegLam, D06, ENRCV, Rep3

value: PegLam  ENRCV


title: lung tissue-CONTROL-CTRL4_r146.111

value: CONTROL


title: XX_D2_REPi_RE57R_Unsorted_R3


title: PegLam, D06, ENRCV, Rep1

description: Library name: PegLam, D06, ENRCV, Rep1

value: Small intestine


title: PegLam, D06, ENRCV, Rep2

description: Library name: PegLam, D06, ENRCV, Rep2

value: Small intestinal organoid


title: lung tissue-IPF-IPF7_r127.15


title: PegLam, D06, ENRCD, Rep3

description: Library name: PegLam, D06, ENRCD, Rep3

value: WT

value: PegLam  ENRCD


title: XX_D2_REPi_RE57R_GFP-Low_R2

value: 2iL-withdrawal/Pooled CRISPRi screen


title: lung tissue-IPF-IPF6_r120.100


title: PegLam, D06, ENRCD, Rep2

description: Library name: PegLam, D06, ENRCD, Rep2


title: PegLam, D06, ENRCD, Rep1

description: Library name: PegLam, D06, ENRCD, Rep1


title: lung tissue-CONTROL-CTRL2_r94.5


title: XX_D2_REPi_RE57R_GFP-High_R2


title: PegLam, D04, ENRCV, Rep2

description: Library name: PegLam, D04, ENRCV, Rep2


title: PegLam, D04, ENRCV, Rep3

description: Library name: PegLam, D04, ENRCV, Rep3


title: lung tissue-IPF-IPF3_r25.15


title: Mat, D06, ENR, Rep3

description: Library name: Mat, D06, ENR, Rep3

value: Mat  ENR


title: XX_D2_REPi_RE57R_Unsorted_R2


title: lung tissue-CONTROL-CTRL5_r6978.339


title: PegLam, D04, ENRCV, Rep1

description: Library name: PegLam, D04, ENRCV, Rep1


title: XX_D2_REPi_RE57R_GFP-Low_R1


title: XX_D2_REPi_RE57R_GFP-High_R1


title: Mat, D06, ENR, Rep2

description: Library name: Mat, D06, ENR, Rep2


title: lung tissue-IPF-IPF2_r11.54


title: Mat, D06, ENRD, Rep2

description: Library name: Mat, D06, ENRD, Rep2

value: Mat  ENRD


title: Mat, D06, ENRD, Rep3

description: Library name: Mat, D06, ENRD, Rep3


title: lung tissue-IPF-IPF4_r50.25


title: XX_D2_REPi_RE57R_Unsorted_R1

value: Embryonic stem cells


title: Mat, D06, ENRCV, Rep3

description: Library name: Mat, D06, ENRCV, Rep3

value: Mat  ENRCV


title: Mat, D06, ENRD, Rep1

description: Library name: Mat, D06, ENRD, Rep1


title: lung tissue-IPF-IPF5_r110.12

value: M


title: Mat, D06, ENRCV, Rep2

description: Library name: Mat, D06, ENRCV, Rep2


title: lung tissue-CONTROL-CTRL1_r62.96

value: lung tissue sample


title: Mat, D06, ENRCD, Rep3

description: Library name: Mat, D06, ENRCD, Rep3

value: Mat  ENRCD


title: Mat, D06, ENRCD, Rep2

description: Library name: Mat, D06, ENRCD, Rep2


title: XX_D2_REPi_RE57M_Unsorted_R3

value: CAST / C57BL/6


title: Mat, D06, ENRCD, Rep1

description: Library name: Mat, D06, ENRCD, Rep1


title: lung tissue-CONTROL-CTRL8_r6989.1771


title: XX_D2_REPi_RE57M_GFP-Low_R2


title: Mat, D04, ENRCV, Rep3

description: Library name: Mat, D04, ENRCV, Rep3


title: Mat, D04, ENRCV, Rep2

description: Library name: Mat, D04, ENRCV, Rep2


title: lung tissue-CONTROL-CTRL7_r6983.2283


title: Mat, D06, ENR, Rep1

description: Library name: Mat, D06, ENR, Rep1


title: XX_D2_REPi_RE57M_GFP-High_R2


title: lung tissue-IPF-IPF10_r190.4

value: IPF


title: NOD1-KO, day8, rep2

city: Tokyo

first: Yoshitaka

last: Kimura

address: Kaga 2-11-1, Itabashi-ku

department: Department of Microbiology and Immunulogy

institute: Teikyo University School of Medicine

description: KO_Day8 - CRS_009_17 (GE)

data_processing:
CLC Genomic Workbench v10.1.1
Assembly: mm10
Supplementary files format and content: excel book file (.xlsx) includes raw counts, normalized counts, and Log2 transformed counst for each sample

source_name: bone marrow-derived dendtiric cell

growth_protocol: 5x10^5 cells of BMDCs derived from NOD1-KO mice and C57BL/6 mice were cultured in 48-well plates in RPMI-1640 supplemented with 10 % heat-inactivated FBS, 50 µmol/L 2-mercaptometanol, and 20 ng/mL murine GM-CSF.

extract_protocol:
The samples were treated with the TRIZOL reagent (Thermo Fisher Scientific, MA, USA). Purified total RNA was resuspended in H2O, and the total RNA was quantified using a Nanodrop spectrophotometer (Thermo Fisher Scientific, MA, USA) and RNA 6000 Pico Kit (Agilent Technologies, CA, USA) for RNA quality control (QC).
Total RNA (500 ng of the quantified RNA) was used for ribosomal RNA (rRNA) depletion using the rRNA-depletion kit (New England Biolabs, MA, USA), followed by directional library synthesis using the NEB Next Ultra Directional RNA Library Prep Kit (New England Biolabs, MA, USA).

treatment_protocol: Cells were collected 0h, 48 h and day8 after stimulation with 100 μg/mL Candida albicans water soluble fractions (CAWS).

value: bone marrow-derived dendtiric cell

value: CAWS, day8


title: NOD1-KO, day8, rep3

description: KO_Day8 - CRS_009_18 (GE)


title: XX_D2_REPi_RE57M_Unsorted_R2


title: WT, day8, rep3

description: WT_Day8 - CRS_009_15 (GE)


title: XX_D2_REPi_RE57M_GFP-Low_R3


title: lung tissue-IPF-IPF9_r162.23


title: NOD1-KO, day8, rep1

description: KO_Day8 - CRS_009_16 (GE)


title: lung tissue-IPF-IPF8_r147.24


title: WT, day8, rep2

description: WT_Day8 - CRS_009_14 (GE)


title: XX_D2_REPi_RE57M_GFP-Low_R1


title: XX_D2_REPi_RE57M_GFP-High_R3


title: Mat, D06, ENRCV, Rep1

description: Library name: Mat, D06, ENRCV, Rep1


title: XX_D2_REPi_RE57M_GFP-High_R1


title: NOD1-KO, day2, rep3

description: KO_Day2 - CRS_009_12 (GE)

value: CAWS, day2


title: WT, day8, rep1

description: WT_Day8 - CRS_009_13 (GE)


title: NOD1-KO, day2, rep2

description: KO_Day2 - CRS_009_11 (GE)


title: XX_D2_REPi_RE57M_Unsorted_R1


title: lung tissue-CONTROL-CTRL4_r146.193

value: CONTROL


title: NOD1-KO, day2, rep1

description: KO_Day2 - CRS_009_10 (GE)


title: lung tissue-IPF-IPF7_r127.29


title: WT, day2, rep3

description: WT_Day2 - CRS_009_09 (GE)


title: XX_D2_REPi_RE57L_GFP-Low_R3


title: WT, day2, rep2

description: WT_Day2 - CRS_009_08 (GE)


title: Mat, D04, ENRCV, Rep1

description: Library name: Mat, D04, ENRCV, Rep1

value: Small intestine

value: Small intestinal organoid


title: lung tissue-CONTROL-CTRL5_r6978.508


title: WT, day2, rep1

description: WT_Day2 - CRS_009_07 (GE)

value: WT


title: XX_D2_REPi_RE57L_GFP-High_R3

value: 2iL-withdrawal/Pooled CRISPRi screen


title: NOD1-KO, day0, rep3

description: KO_Day0 - CRS_009_06 (GE)

value: untreated, day0


title: NOD1-KO, day0, rep2

description: KO_Day0 - CRS_009_05 (GE)


title: XX_D2_REPi_RE57L_Unsorted_R3


title: XX_D2_REPi_RE57L_GFP-Low_R2


title: lung tissue-IPF-IPF3_r25.51


title: lung tissue-IPF-IPF4_r50.18


title: WT, day0, rep3

description: WT_Day0 - CRS_009_03 (GE)


title: NOD1-KO, day0, rep1

description: KO_Day0 - CRS_009_04 (GE)


title: lung tissue-IPF-IPF6_r120.23


title: KP dSPHK1 #4 + FCS

city: Vienna

first: Herwig

middle: P

last: Moll

address: Waehringer Strasse 13a

country: Austria

institute: Medical University of Vienna

data_processing:
Reads in fastq format were aligned to the mouse reference genome version GRCh38 with Gencode mV23 annotations using STAR aligner version 2.6.1a in 2-pass mode. Reads per gene were counted by STAR.
Assembly: Reads in fastq format were aligned to the mouse reference genome version GRCh38 with Gencode mV23 annotations using STAR aligner version 2.6.1a in 2-pass mode. Reads per gene were counted by STAR.
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

source_name: lung

extract_protocol:
RNA was harvested using Rneasy Mini kit (QIAGEN)
Sequencing libraries were be prepared at the Core Facility Genomics, Medical University of Vienna using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina according to manufacturer's protocols (New England Biolabs).

value: lung

value: KP lung adenocarcinoma


title: WT, day0, rep2

description: WT_Day0 - CRS_009_02 (GE)


title: WT, day0, rep1

description: WT_Day0 - CRS_009_01 (GE)


title: XX_D2_REPi_RE57L_GFP-High_R2

value: Embryonic stem cells


title: lung tissue-IPF-IPF5_r110.1

value: M


title: KP dSPHK1 #3 + FCS


title: Dental pulp cKO_4

city: Houston

first: Wenbo

last: Chen

address: 7000 Fannin Street

institute: The University of Texas Health Science Center at Houston

description: FACS-sorted, tamoxifen at P3

data_processing:
Quality control and adapter trimming were conducted on the raw sequencing reads using Trim Galore.
Trimmed sequence reads were mapped to the mouse reference genome (GENCODE GRCm39) using STAR.
Raw read counts were extracted from STAR alignment.
Assembly: GRCm39/mm39
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample

source_name: Dental pulp (mandibular molars)

extract_protocol:
Mandibular molars were extracted, dental follicle cells were enzymatically dissociated and tdTomato+ cells were FACS-isolated. Total RNA was isolated using PicoPure RNA isolation kit and cDNA was prepared by SMART-Seq v4 Ultra Low Input RNA kit for Sequencing.
SMART-Seq V4 PLUS Kit

value: Dental pulp (mandibular molars)

value: CXCL12+ apical papilla cells


title: XX_D2_REPi_RE57L_Unsorted_R2

value: CAST / C57BL/6


title: KP dSPHK1 #2 + FCS


title: Dental pulp cKO_3

description: FACS-sorted, tamoxifen at P3


title: XX_D2_REPi_RE57L_GFP-Low_R1


title: Dental pulp cKO_2

description: FACS-sorted, tamoxifen at P3


title: lung tissue-CONTROL-CTRL5_r6978.524

source_name: lung tissue sample

value: lung tissue sample


title: lung tissue-CONTROL-CTRL1_r62.46


title: KP dSPHK1 #4


title: XX_D2_REPi_RE57L_Unsorted_R1


title: lung tissue-IPF-IPF10_r190.22

value: IPF


title: Dental pulp cKO_1

description: FACS-sorted, tamoxifen at P3


title: KP dSPHK1 #3


title: XX_D2_REPi_noRE_GFP-Low_R3


title: lung tissue-IPF-IPF6_r120.4


title: XX_D2_REPi_noRE_GFP-High_R3


title: lung tissue-IPF-IPF1_r3.28


title: Dental pulp cHet_3

description: FACS-sorted, tamoxifen at P3


title: XX_D2_REPi_noRE_Unsorted_R3


title: lung tissue-IPF-IPF3_r25.47a


title: lung tissue-CONTROL-CTRL8_r6989.1992


title: KP dSPHK1 #1


title: lung tissue-IPF-IPF2_r11.6


title: Dental pulp cHet_1

description: FACS-sorted, tamoxifen at P3


title: Dental pulp cHet_2

description: FACS-sorted, tamoxifen at P3


title: XX_D2_REPi_noRE_GFP-Low_R2


title: KP ctrl #3 + FCS


title: XX_D2_REPi_noRE_GFP-High_R2


title: KP ctrl #4 + FCS


title: KP dSPHK1 #1 + FCS


title: TFiMini_PlasmidLibrary

description:
Plasmid
TFiMini.count.txt
TFiMini.count_normalized.txt

organism: synthetic construct


title: XX_D2_REPi_RE57L_GFP-High_R1


title: lung tissue-CONTROL-CTRL7_r6983.758


title: XX_D2_REPi_noRE_Unsorted_R2


title: lung tissue-IPF-IPF4_r50.4


title: KP ctrl #2 + FCS


title: XX_D2_REPi_noRE_GFP-Low_R1


title: KP ctrl #1 + FCS


title: 75 div

city: Irvine

first: Edwin

middle: S

last: Monuki

address: 845 Health Science Road

department: Experimental Pathology

institute: University of California Irvine

description:
Library name: Sample 4
10X Genomics

data_processing:
FASTQ files were processed and mapped to the reference genome GRCh38 through Cell Ranger. Briefly, genes expressed in <10 cells were excluded, and cells with 1000-6000 genes/cell and <12.5% mitochondrial gene expression were included. The four time points were tested for their batch effect through two batch correction methods; RPCA and SCTransform with the Seurat platform. Datasets post quality control were combined with the merge function in Seurat while the time point of origin was retained in the metadata. RPCA batch correction was done with default settings of features to consider (2000) and plotted as a UMAP with color coding by time point of origin showing similar display of cells to the non-corrected. SCTransform batch correction was done with default settings of features to consider (all) and plotted as a UMAP with color coding by time point of origin showing similar display of cells to the non-corrected. Due to the similar grouping of cells in batch and non-batch corrected data, non-batch corrected data was used for further processing with the SoptSC platform.
Assembly: Human
Assembly: GRCh38
Supplementary files format and content: Tab seperated value files and matirx files

source_name: H1 derived cells

extract_protocol:
For each timepoint, two wells of a 4-well chamber slide were dissociated and pooled. The selected protocol involved dissociating with warm TrypLE (Thermo Fisher #12605010) for 25 minutes at 37C, resuspending in FACS buffer at RT (0.02% BSA in DPBS), then propidium iodine was added for 10 minutes (Thermo Fisher #P1304MP) before placing on ice. FACS for single live cells was performed by the UCI Flow Cytometry Core using a FACSAria II (BD Biosciences).
Single cell capture with the 10x Chromium platform, cDNA library preparation, and cDNA QC analysis (Qubit dsDNA HS Assay kit (Life Technologies Q32851) and high sensitivity DNA chips (Agilent. 5067-4626)) were performed by the UCI Genomics Research and Technology Hub (GRT Hub). Library generation was done with a V2 chemistry kit and an average capture of ~10,000 barcoded cells, per user guide (CG00052 Rev B). The cDNA libraries were sequenced using the HiSeq 4000 platform (Illumina) to achieve an average depth of 50,000 reads per cell and 2,500 genes per cell.

value: H1 derived cells

value: APOE 3/3


title: 55 div

description:
Library name: Sample 3
10X Genomics


title: lung tissue-CONTROL-CTRL2_r94.27

value: CONTROL


title: KP dSPHK1 #2


title: Dental pulp cHet_4

description: FACS-sorted, tamoxifen at P3


title: KP ctrl #4


title: lung tissue-IPF-IPF3_r25.49


title: XX_D2_REPi_noRE_GFP-High_R1

data_processing:
*library strategy: Pooled CRISPR screen
Count tables were generated using MAGeCK (v0.5.9.3) with [mageck count –norm-method control](Li et al. 2014).
39 Guides with low expression in the unsorted population (≤150 mean normalized counts) were removed from the analysis. Guides targeting Zfp866 were removed from the analysis since their sequence overlapped with guides targeting Gm20422. Only guides with more than 150 mean counts in the unsorted samples were used for analysis.
The noRE reporter screen was analyzed separately in order to identify interactions of targeted TFs with the FIREWACh minimal promoter. Significant enrichment or depletion was detected using an unpaired t-test between the normalized counts in the GFPHigh and GFPLow populations, followed by multiple testing correction (FDR<0.2). 7 TF targets (Nfrkb, Sall4, Ctcf, Zfp296, Zfp236, Sp1 and E2f4)  were removed from further analysis due to their effect on the noRE reporter line.
Interaction scores for the assayed TF-RE interactions were calculated as z-scores across all GFPHigh/GFPLow log2 fold changes, as done before for CRISPR screen data(Xu et al. 2021). This was done to correct for differences in observed effect sizes between the reporter lines. In detail, mean GFPHigh/GFPLow log2 fold changes were calculated for all guide/reporter combinations. Each log2 fold change was then normalized by subtracting the mean log2 fold change across each target from the noRE reporter results. The corrected fold changes were scaled using a z-score transformation and determined as interaction scores. Significance was calculated using a one-sample t-test with [t.test(mu=0)], followed by multiple testing correction with [p.adjust()].
Assembly: mm10
Supplementary files format and content: Count tables (.txt)
Supplementary files format and content: Normalized count tables (.txt)
Supplementary files format and content: Interaction scores (.txt)


title: 46 div

description:
Library name: Sample 2
10X Genomics


title: lung tissue-CONTROL-CTRL5_r6978.525


title: XX_D2_REPi_noRE_Unsorted_R1


title: lung tissue-IPF-IPF6_r120.16


title: KP ctrl #2