title: mbf1c_Deacc2_Exp3


title: R9-ILC-41

status: Public on Sep 30 2022

type: SRA

city: Guangzhou, China

first: yunqing

last: Lin

address: Building 3, No.188 Kaiyuan Avenue, Huangpu District, Guangzhou

department: Center for Cell Lineage and Atlas (CCLA)

country: China

institute: Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)

library_source: transcriptomic

data_processing:
Bcl2fastq (verison 2.16.0.10) convert .bcl files into fastq files
Fastq files were aligned to mm10 genome.*.ht2 files to generate *.sam file by HISAT2 (version 2.1.0). And the used samtools (version 0.1.19) to convert and sort the sam file to bam file. StringTie (version 1.3.4) were used to calculated genes expression level in TPM.
Gene expression levels in TPM of different samples were normalized by Stringtie.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with TPM value for every gene and every cell

molecule: polyA RNA

organism: Mus musculus

source_name: Innate lymphoid cells

growth_protocol: The single regenerative R9-ILCs were sorted from the intestine of Rag2-/-Il2rg-/- recipient mice 3 weeks after transplantation and the WT-ILCs were sorted from the intestine of wild type mouse (C57BL/6, CD45.2 strain, 8-week-old) by folw cytometry.

extract_protocol:
The procedure of RNA extraction and reverse transcription into double-stranded DNA were prepared using Discover-sc WTA Kit V2 (Vazyme, N711)
Libraries were prepared according to instruction of TruePrepTM  DNA Library Prep Kit V2 (Vazyme,TD503).

treatment_protocol: The single ILCs were sorted for RNAseq analysis.

tag: strain

tag: time

value: 3 weeks after transplantation

tag: tissue

value: intestine of recipients

tag: cell type

value: Innate lymphoid cells


title: Col0_Deacc2_Exp3

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

country: Germany

institute: MPI of Molecular Plant Physiology

data_processing:
mapping: Read mapping was performed using STAR v2.6.0c against the A. thaliana reference genome Col-0, release Ensembl39 based on TAIR10 version 39, which included the Araport11 annotation.
read normalization: Raw counts were extracted from the STAR ReadsPerGene output files and filtered by removing lowly expressed genes with a sum smaller than 10 counts per gene across all conditions. The RNA-Seq counts were normalized by the method included in the DESeq2 package
Genome_build: EnsemblPlants version 39 of Arabidopsis thaliana
Supplementary_files_format_and_content: Default STAR output files (ASCII format): Gene identifier, Read count (unstranded RNA-seq), Read count (counts for the 1st read strand aligned with RNA), Read count (counts for the 2nd read strand aligned with RNA)

molecule: total RNA

organism: Arabidopsis thaliana

source_name: whole rosettes

growth_protocol: Plant lines were grown on soil in a climate chamber with 20°C day-time temperature and 6°C night-time temperature with a light intensity of 180 µE m-2 s-1 in a 14 h light cycle and a humidity of 60% at day and 70% at night. Plants were moved to a short day-climate chamber after one week of growth with the following conditions: 20°C/16°C day/night, 60%/75% humidity day/night, 8 h day length with 180 µE m-2 s-1. The plants were kept under short-day conditions for one week of short-day before being pricked (10 plants in one 10 cm pot). After pricking plants were grown one further week at short-day conditions and then transferred to long-day conditions (20°C day and 16°C night temperature with a day length of 16 h at a light intensity of 200 μE m-2 s-1).

extract_protocol:
Total RNA was isolated by a "single-step" Trizol based method. DNAse treatment was carried out on 4 µg of RNA and the removal of DNA was validated by qPCR using intron-specific primers. RNA integrity was validated by an Agilent 2100 Bioanalyzer.
Library preparation and RNA sequencing (RNA-Seq) was carried out at BGI Genomics and performed according to the BGISEQ-500 workflow.

treatment_protocol: 28 days old Arabidopsis rosettes were used for cold acclimation and deacclimation experiments. For cold acclimation, plants were transferred to 4°C for 3 days with light intensity of 90 µE m-2 s-1 and 16 h day length and humidity of 70-80%. For deacclimation plants were moved back to long-day conditions for up to 4 days. Arabidopsis rosettes were harvested before (NonA) or after cold acclimation (ACC) either and for deacclimation either daily with an even tighter time course in the first 24 h (Deacc2h to Deacc96h) or after two (Deacc2) or four days (Deacc4) of deacclimation as shown in Figure 1 and frozen immediately in liquid nitrogen.

tag: condition

tag: plant line

tag: replicate

value: whole rosettes


title: Pooled GEX library for 8 lung organoids_2

city: San Francisco

first: Arjun

middle: Arkal

last: Rao

state: CA

address: 505 Parnassus Ave, S-447

department: CoLabs

country: USA

institute: University of California, San Francisco

description:
processed data file contains LMO counts from roose-2_MSQ
roose-2_GEX

library_source: transcriptomic single cell

data_processing:
sequencer-generated bcl files were converted to fastqs using the cellranger mkfastq (cellranger version 4.0.0) command with default parameters.
Gene expression fastq files were aligned to the Human  reference genome (with ENSEMBL v85 annotation), and MultiSeq Barcoding fastqs were counted against a reference of all possible MultiSeq barcodes using cellranger count (cellranger version 4.0.0) and default parameters.
MultiSeq Barcoding fastqs were counted against a reference of all possible MultiSeq barcodes using cellranger count (cellranger version 4.0.0).
Assembly: GRCH38.p7
Supplementary files format and content: H5ad formatted raw feature-barcode matrices produced by cellranger

organism: Homo sapiens

source_name: lung

growth_protocol: Lung organoids were generated from lung ressections using the protocol described in Sachs et al, 2019

extract_protocol:
For the single-cell RNA sequencing experiments each organoid was generated from 4 different donors. After organoid dissociation into single-cell suspension using TrypLE express (ThermoFisher Scientific Cat#12604012), cells were counted, and pooled together (78,000 total cells).
Pooled cells were then loaded evenly across two lanes in the Chromium Controller for generating single-cell contained in lipid droplets following the manufacturer’s instructions (10X Genomics). A Chromium Single cell 3’ Reagent Kit (v3.1) (10X Genomics) was used for reverse transcription, cDNA amplification and library construction of the gene expression libraries following the manufacturer’s instructions. All samples were encapsulated, and cDNA was generated within 6 hours after organoid processing. MULTISeq barcode libraries were generated using the protocol describedin Mcginnis et.al, Nature Methods (2019). Finally, Pooled libraries were sequenced on an Illumina NovaSeq 6000.
roose-1/2_GEX: 10X 3' Gene Expression; roose-1/2_MSQ: MULTI-Seq tagging of Single Cells using Lipid Barcodes

treatment_protocol: Lung organoids were removed from Matrigel following 1 minute incubation with Dispase 0.5U/ml (StemCell Technologies, Cat #07913), carefully transferred into a 15 ml tube, washed with DPBS (UCSF Cell Culture Facility) supplemented with 5 mm EDTA (Cellgro, Cat#46-034-CI) and pelleted (200g, 3 minutes at Room Temperature). Organoid pellets were resuspended in 500 µl of lung organoid media. Virus was added at MOI=0.15 for H1N1/PR8 mCherry and MOI=0.3 for SARS-CoV-2. Every organoid well contained 10,000 cells. After 2 hours of incubation, lung organoids were washed twice with PBS and resuspended in 300μL Matrigel (Corning) and plated in ~50 μL droplets in a 24 well tissue culture plate. Plates were placed at 37 degrees Celsius with 5% CO2 for 20 min to solidify the Matrigel droplets upon which 550uL of lung organoid media was added to each well. Plates were incubated in the standard tissue culture incubator at 37 degrees Celsius for 92 hours.

value: lung

tag: model

value: organoid

tag: treatment

value: 4 mock + 4 infected with SARS-SoV-2


title: Pooled LMO library for 8 lung organoids_1

description:
MultiSeq Barcode map: MultiSeq-Barcode13=2478_Mock,MultiSeq-Barcode14=2478_SARS_CoV_2,MultiSeq-Barcode15=2522_Mock,MultiSeq-Barcode16=2522_SARS_CoV_2,MultiSeq-Barcode17=2524_Mock,MultiSeq-Barcode18=2524_SARS_CoV_2,MultiSeq-Barcode19=Lung_7_Mock,MultiSeq-Barcode20=Lung_7_SARS_CoV_2
roose-1_MSQ

library_source: other

molecule: other


title: Pachynema RNA-seq rep 3

city: Ithaca

first: Charles

last: Danko

state: NY

address: 235 Hungerford Hill Rd

institute: Cornell University

data_processing:
Reads were trimmed for low quality and adaptor sequences with cutadapt v1.8; parameters: -m 50 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAG --match-read-wildcards.
Reads were mapped to the reference genome (mm10.rRNA.fa.gz) using STAR v2.5.3a
Mapped reads were converted to bigWig format using BedTools.
To normalize for sequencing depth, libraries were scaled using reads per kilobase per million mapped reads (RPKM).
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Prophase I substages

extract_protocol:
Prophase I substages were isolated using STAPUT. 1 million cells were used as input to extra total RNA. Immediately following STAPUT, testicular cells were lysed with TrizolLS (Thermo Fisher). Total RNA was purified using TrizolLS according to the commercial protocol with the following additions: after the first phase separation, an additional chloroform extraction step of the aqueous layer was performed using Phase-lock Gel heavy tubes (Quanta Biosciences); addition of 1ul Glyco-blue (Thermo Fisher) immediately prior to isopropanol precipitation; two washes of the RNA pellet with 75% ethanol. If the RNA integrity results indicated co-purified genomic DNA, it was removed with the RapidOUT DNA Removal kit (Thermo Fisher). RNA sample quality was confirmed by spectrophotometry (Nanodrop) to determine concentration and chemical purity (A260/230 and A260/280 ratios) and with a Fragment Analyzer (Advanced Analytical) to determine RNA integrity.
PolyA+ RNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). TruSeq-barcoded RNAseq libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). Each library was quantified with a Qubit 2.0 (dsDNA HS kit; Thermo Fisher) and the size distribution was determined with a Fragment Analyzer (Advanced Analytical) prior to pooling. Libraries were sequenced on a NextSeq500 instrument (Illumina). At least 20M single-end 75bp reads were generated per library.

value: Prophase I substages

tag: developmental stage

value: Pachynema

tag: genotype

value: WT


title: R9-ILC-40


title: Col0_Deacc4_Exp3


title: Healthy donor 3 -anti-CD96 mAb treatment [HD3_19_134]

city: Southampton

first: Aymen

last: Al-Shamkhani

address: Tremona Road

department: School of Cancer Sciences

country: United Kingdom

institute: University of Southampton

data_processing:
Quality control analysis of the RNA-Seq data was conducted using FastQC
Alignment: Sequenced reads from each sample and run were aligned to the human genome (primary assembly, GRCh38.p12, GCA_000001405.27) using the STAR alignment algorithm (version 2.5.2b, default parameters).
Counts: Uniquely-mapped alignments overlapping gene exons were counted using feature Counts from the Rsubread package (version 1.32.4). Counting was performed relative to Ensembl 97 (Jul 2019) gene annotation and counts summarized at the gene level. Rsubread parameters: countMultiMappingRead=FALSE, isPairedEnd=TRUE.
Genome_build: GRCh38.p12, GCA_000001405.27
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: peripheral blood mononuclear cells

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus Mini kit. The purity, concentration and integrity of the RNA were assessed using a Nanodrop Spectrophotometer (Thermo Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: T cells

value: anti-CD96 mAb

tag: subject status/id

value: Healthy donor 3


title: R9-ILC-4


title: Leptonema/Zygonema RNA-seq rep 3

value: Leptonema/Zygonema


title: jub1_ACC_Exp3

value: ACC


title: Leptonema/Zygonema RNA-seq rep 2


title: Leptonema/Zygonema RNA-seq rep 1


title: Col0_ACC_Exp3


title: mbf1c_ACC_Exp3


title: Pachynema RNA-seq rep 1


title: R9-ILC-38


title: Healthy donor 2 -isotype control mAb treatment [HD2_isotype]

value: isotype control mAb

value: Healthy donor 2


title: Healthy donor 1 -anti-CD96 mAb treatment [HD1_19_134]

value: Healthy donor 1


title: 12_mTEC_LOX_E18_5_3

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

description: Pregnant female

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.5.1b.
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version M13 (based on Ensembl 88).
Expression values were also computed using RSEM version 1.2.28 based on Gencode version M13 transcript annotations.
Assembly: GRCm38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned.
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column).

source_name: medullary thymic epithelial cell

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106).
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

value: Klf4 WT :B5t-WT/WT :Klf4 lox/lox

tag: Sex

value: Female

value: Pregnant

tag: age

value: 12 weeks

value: Thymus

value: mTEC (EpCAM+, CD45-, UEA1+)


title: mbf1c_NonA_Exp3

value: NonA

value: whole rosettes


title: Healthy donor 2 -anti-CD96 mAb treatment [HD2_19_134]


title: R9-ILC-35

value: 3 weeks after transplantation

value: intestine of recipients

value: Innate lymphoid cells


title: jub1_NonA_Exp3


title: 09_mTEC_KO_E18_5_3

description: Pregnant female

value: Klf4 KO :B5t-iCre/WT :Klf4 -/-


title: Alveolar oragnoids_Dam-NKX2.1 [14996]

city: Cambridge

first: Kyungtae

last: Lim

address: Tennis Court Road

department: The Wellcome Trust/Cancer Research UK Gurdon Institute

institute: University of Cambridge

description: Alveolar differentiation for day 7_Dam-NKX2.1

library_source: genomic

data_processing:
Library strategy: DamID-seq
Illumina software used for conventional basecalling.
Reads were mapped to a bowtie2 indexed GRCh38 genome assembly (hg38), binned into 5’-GATC-3’ fragments.
NKX2-1 fusion samples were normalized against a paired Dam-only control derived from the same biological sample (RPM normalization, 300 bp bins)
Macs2 (v2.1.2) was used to call broad peaks for each NKX2-1 fusion and Dam-only pair using the bam files generated by the damidseq_pipeline.
Peaks were filtered to only those present in 2/3 replicates using bedtools (v2.26.0) and surpassing FDR<10-5
Genome_build: GRCh38 genome assembly (hg38)
Supplementary_files_format_and_content: A bigwig file (.bw format) for each NKX2-1 fusion samples normalized against a paired Dam-only control derived from the same biological sample

molecule: genomic DNA

source_name: Human fetal lung

growth_protocol: Fetal lung tip organoids were cultured in self-renweing condition, or in alveolar differentiation medium containing DAPT, DCI, SB431542, and CHIR for 1 week

extract_protocol:
Genomic DNA was extracted and processed as previously described (Marshall et al., 2016).
See method and Marshall et al., 2016

treatment_protocol: 200K of CD44+ cells sorted from pseudoglandular organoids, CD36+/CD44+ cells sorted from LinPOS organoids, or single cell dissociated alveolar organoids were infected with lentivirus habouring 'mNeonGreen-Dam (Dam only)' or 'mNeonGreen-Dam-NKX2.1' for 48 hours.

tag: sample id

tag: developmetal age

value: 21 pcw

tag: passage number


title: 11_mTEC_LOX_E18_5_2

description: Pregnant female


title: Alveolar oragnoids_Dam only [14556]

description: Alveolar differentiation for day 7_Dam only

value: 20 pcw


title: Alveolar oragnoids_Dam only [14996]


title: Col0_NonA_Exp3


title: 10_mTEC_LOX_E18_5_1

description: Pregnant female


title: mbf1c_Deacc4_Exp2


title: Alveolar oragnoids_Dam-NKX2.1 [14556]


title: R9-ILC-30

tag: strain


title: R9-ILC-39

tag: time


title: R9-ILC-37

tag: tissue


title: R9-ILC-33

tag: cell type


title: R9-ILC-31


title: jub1_Deacc4_Exp2

tag: condition


title: Healthy donor 1 -isotype control mAb treatment [HD1_isotype]

value: T cells

value: isotype control mAb


title: 07_mTEC_KO_E18_5_1

description: Pregnant female


title: R9-ILC-3


title: 08_mTEC_KO_E18_5_2

description: Pregnant female


title: Col0_Deacc4_Exp2

tag: plant line


title: mbf1c_Deacc2_Exp2

tag: replicate


title: 06_cTEC_LOX_E18_5_3

description: Pregnant female

source_name: cortical thymic epithelial cell

value: cTEC (EpCAM+, CD45-, UEA1-)


title: CD36+CD44+_LinPOS organoids_Dam only [14996]

description: CD36+CD44+ population in vitro_Dam only


title: R9-ILC-28


title: jub1_Deacc2_Exp2


title: 05_cTEC_LOX_E18_5_2

description: Pregnant female

value: Klf4 WT :B5t-WT/WT :Klf4 lox/lox


title: R9-ILC-29


title: mbf1c_ACC_Exp2

value: ACC


title: Alveolar oragnoids_Dam only [14404]

value: 19 pcw


title: CD36+CD44+_LinPOS organoids_Dam-NKX2.1 [14556]

description: CD36+CD44+ population in vitro_Dam-NKX2.1


title: R9-ILC-22


title: 04_cTEC_LOX_E18_5_1

description: Pregnant female

value: Female

value: Pregnant

value: 12 weeks


title: CD36+CD44+_LinPOS organoids_Dam-NKX2.1 [14459]


title: R9-ILC-27


title: R9-ILC-25


title: mTEC_LOX_F_3

description: Non-pregnant female

value: Non-pregnant

value: Thymus

value: mTEC (EpCAM+, CD45-, UEA1+)


title: R9-ILC-24

value: 3 weeks after transplantation

value: intestine of recipients


title: 01_cTEC_KO_E18_5_1

description: Pregnant female

value: Klf4 KO :B5t-iCre/WT :Klf4 -/-


title: CD36+CD44+_LinPOS organoids_Dam-NKX2.1 [14996]

value: 21 pcw


title: CD36+CD44+_LinPOS organoids_Dam only [14556]

description: CD36+CD44+ population in vitro_Dam only

value: 20 pcw


title: R9-ILC-21

value: Innate lymphoid cells


title: CD36+CD44+_LinPOS organoids_Dam only [14459]

description: CD36+CD44+ population in vitro_Dam only


title: Alveolar oragnoids_Dam-NKX2.1 [14404]


title: jub1_NonA_Exp2

value: NonA

value: whole rosettes


title: Col0_ACC_Exp2


title: jub1_ACC_Exp2


title: 02_cTEC_KO_E18_5_2

description: Pregnant female

value: cTEC (EpCAM+, CD45-, UEA1-)


title: mTEC_LOX_F_2

description: Non-pregnant female

value: Klf4 WT :B5t-WT/WT :Klf4 lox/lox


title: Col0_Deacc2_Exp2


title: 03_cTEC_KO_E18_5_3

description: Pregnant female


title: CD44+_ Pseudoglandular organoids_Dam only [1943]

description: CD44+ population in vitro_Dam only

value: 8 pcw


title: mbf1c_NonA_Exp2


title: CD44+_ Pseudoglandular organoids_Dam-NKX2.1 [1943]

description: CD44+ population in vitro_Dam-NKX2.1


title: CD44+_ Pseudoglandular organoids_Dam only [1938]

description: CD44+ population in vitro_Dam only

value: 9 pcw


title: mbf1c_Deacc4_Exp1


title: R9-ILC-17


title: R9-ILC-19


title: jub1_Deacc4_Exp1


title: Col0_Deacc4_Exp1


title: R9-ILC-20


title: R9-ILC-15


title: CD44+_ Pseudoglandular organoids_Dam only [1915]

description: CD44+ population in vitro_Dam only


title: Col0_NonA_Exp2


title: jub1_Deacc2_Exp1


title: CD44+_ Pseudoglandular organoids_Dam-NKX2.1 [1938]

description: CD44+ population in vitro_Dam-NKX2.1


title: R9-ILC-16


title: R9-ILC-14


title: mTEC_LOX_F_1

description: Non-pregnant female

value: Female


title: CD44+_ Pseudoglandular organoids_Dam-NKX2.1 [1915]

description: CD44+ population in vitro_Dam-NKX2.1


title: mbf1c_Deacc2_Exp1


title: mTEC_KO_F_1

description: Non-pregnant female

value: 12 weeks


title: R9-ILC-13


title: mTEC_KO_F_2

description: Non-pregnant female

value: Non-pregnant


title: cTEC_LOX_F_2

description: Non-pregnant female

value: Thymus


title: Human right atrium_1

city: Munich

first: Harald

last: Lahm

address: 36, Lazarettstraße

department: INSURE

institute: German Heart Center Munich

data_processing:
The libraries generated according to the 10X Genomics protocol v3 were sequenced, demultiplexed and converted to fastq format by EMBL Heidelberg Genomics Core Facilty.
The sequencing parameters were: 28 bp for read1, 8 bp for the index, and 56 bp for informative read2.
The fastq-files were processed with the CellRanger v3 pipeline with standard parameters except for 'pre-mrna' reference file according to the 10x Genomics support file
Gene expression matrix files were subjected to standard Seurat downstream analysis
Genome_build: hg19 GRCh38

molecule: nuclear RNA

source_name: atrium

extract_protocol:
Tissue samples were minced and nuclei extracted in lysis buffer containing 5 mM CaCl2, 3 mM magnesium actetate, 2 mM EDTA, 0.5 mM EGTA, 10 mM Tris, 0.2%, Triton X-100, protease inhibitors and DTT. Nuclei were centrifuged in 1 M sucrose and resuspended in PBS. After staining with Draq7, samples were purified by fluorescence-activated nuclei sorting (FANS). Nuclei were counted under the microscope.
Barcoding, cDNA amplification and gene expression library construction were done using 10x Genomics Chromium Next GEM Single cell 3' Solution v3 according to the manufacturer's recommendation.

treatment_protocol: snap-fozen in liquid nitrogen

value: atrium

tag: compartment

value: nucleus

value: heart


title: Col0_Deacc2_Exp1


title: mTEC_KO_F_3

description: Non-pregnant female

value: Klf4 KO :B5t-iCre/WT :Klf4 -/-

value: mTEC (EpCAM+, CD45-, UEA1+)


title: Human right atrium_2


title: cTEC_LOX_F_1

description: Non-pregnant female


title: mbf1c_ACC_Exp1

value: ACC


title: R9-ILC-10

value: 3 weeks after transplantation

value: intestine of recipients

value: Innate lymphoid cells


title: cTEC_LOX_F_3

description: Non-pregnant female

value: cTEC (EpCAM+, CD45-, UEA1-)


title: R9-ILC-11


title: cTEC_KO_F_3

description: Non-pregnant female


title: cTEC_KO_F_2

description: Non-pregnant female


title: Human left ventricle_2

source_name: interventricular septum

value: interventricular septum


title: jub1_ACC_Exp1

value: whole rosettes


title: Human left ventricle_1


title: RNAseq DIDO3 MUT rep2

status: Public on Sep 29 2022

city: Madrid

first: Tirso

last: Pons

state: Madrid

address: C/ Darwin 3

department: Inmunology and Oncology

country: Spain

institute: Centro Nacional de Biotecnologia

data_processing:
Sequenced reads were mapped to mm10 whole genome using BWA-MEM 0.7.15 with parameters mem -M -t 4 mm10bwaidx file_1.fastq file_2.fastq
The sequences aligned in blacklisted regions  (sites.google.com/site/anshulkundaje/projects/blacklists) were removed with the Intersect tool from BEDTools before calculating accessible regions of chromatin using the MACS2 program
For the calculation of the differential accessibility of chromatin, the accessible and equivalent regions were analyzed with HOMER
The allocation of genes, promoters, UTRs, introns and exons to the accessible regions was carried out with the ChIPseeker program
StringTie was used for assembling RNA-seq alignments into potential transcripts, and also getting count and normalize reads with parameters -e -v -p 32 -G knownGene_UCSC_mm10.gtf
Differentially expressed genes were defined with edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include ChIPseeker annotations of the accessible regions determined with HOMER and MACS2 for each sample
Supplementary_files_format_and_content: tab-delimited text files include cov, FPKM, and TPM values for each sample

source_name: mouse hematopoietic precursors

extract_protocol:
Pre-B cells, extracted from the bone marrow of wt and Dido1dE16 mice, were isolated by sorting
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA was purified by using RNeasy mini plus kit (Qiagen) and their massive sequencing was performed in BGI Genomics (Hong-Kong)

value: hematopoietic precursors

value: DIDO3_exon16 mutant


title: RNAseq DIDO3 MUT rep1


title: RNAseq DIDO3 WT rep1

value: wild type


title: RNAseq DIDO3 WT rep2


title: R9-ILC-1


title: cTEC_KO_F_1

description: Non-pregnant female

value: Female

value: Non-pregnant

value: 12 weeks


title: THP1_Cas13d_pooledScreen wtDR MOI-0 25 CD14_low

city: New York

first: Hans-Hermann

last: Wessels

address: 101 Avenue of the Americas

institute: New York Genome Center

description:
guide RNA library: read1 file contains guide RNA sequence
guide RNA sequence
none
THP1_Cas13d_pooledScreen.counts.csv.gz

data_processing:
Sequencing reads coming from the mRNA library were mapped to a joined genome reference of hg38 (ensemble v97) and mm10 using the Cellranger Software (v3.0.1), or to hg38 using Cellranger v6.0.0 for the THP1 experiment. Barcode guide RNA library reads were mapped simultaneously to a barcode reference using Cellranger. To generate count matrices for HTO and ADT libraries, the CITE-seq-count package (v1.4.2) was used (https://github.com/Hoohm/CITE-seq-Count). Count matrices were then used as input into the Seurat R package (v4.0) to perform all downstream analyses
Assembly: hg38, mm10
Library strategy: CaRPool-seq (Cas13 RNA Perturb-seq)

source_name: blood

extract_protocol:
Puromycin selected, perturbed cells were stained with experiment-specific Antibody Derived Tags (ADT) and barcoded with a unique Oligonucleotide Hash Tag (HTO). After Hash- and Cite-tagged cells were counted and checked for viability using a hematocytometer, cells were loaded into a Chromium Controller (10X Genomics).
Gene expression (GEX) libraries were prepared using Chromium Single Cell 3ʹ v3 protocol (10x Genomics). sgRNA (GDO) libraries from direct capture perturb-seq experiments were prepared using the standard feature barcoding  Chromium Single Cell 3ʹ v3 (10x Genomics) workflow. Cellular ADT and HTO libraries were prepared as described on cite-seq.com (CITE-seq_and_Hashing_protocol_190213). CaRPool-seq bcgRNA libraries were prepared as follows:
Library construction for bcgRNA derived oligos largely followed 10x Genomics user guide CG000184 Rev C for Feature Barcoding with some modifications. Specifically, we eluted the GEM-RT in 33ul and added 2µl containing 0.4µM ADT additive primer (for bcgRNAs and ADTs) and 0.2µM HTO additive primer prior to cDNA amplification. The cDNA was purified using 0.6x SPRI cleanup for mRNA fraction. The supernatant containing ADT, HTO, and bcgRNA cDNA was purified was purified by adding another 1.4x SPRI (0.6+1.4 = 2x SPRI) followed by an additional 2x SPRI clean up. The purified short fragments were split evenly into three pools (e.g. 3 x 20µl). One pool each was used for HTO and ADT library construction as described below. Half of the remaining pool (10µl) was used to construct the bcgRNA library using two PCR recipes. PCR1 adds Illumina P5 and P7 handles to the bcgRNA amplicon (100µl PCR1: 50µl 2x KAPA Hifi PCR Mastermix, up to 45µl bcgRNA PCR template, 2.5µl Feature SI Primers 2 10µM, 2.5µl TruSeq Small RNA RPIx primer (containing i7 index) 10µM; 95°C 3min, 12x[95°C 20sec, 60°C 8sec, 72°C 8sec], 72°C 1min). PCR2 amplifies with P5 and P7 primers (100µl PCR2: 50µl 2x KAPA Hifi PCR Mastermix, up to 45µl purified PCR1 product, 2.5µl P5 primer 10µM, 2.5µl P7 primer 10µM; 95°C 3min, 4x[95°C 20sec, 60°C 8sec, 72°C 8sec], 72°C 1min). The final bcgRNA amplicon has a length of 203bp and can be sequenced on a standard Illumina sequencing platform with standard Illumina sequencing primers (>= 28 cycles Read1 and >=15 cycles Read 2).

value: blood

value: Monocyte isolated from peripheral blood from an acute monocytic leukemia patient

tag: library type

value: Cas13d gRNA amplicon

tag: antibodies/tags


title: THP1_Cas13d_pooledScreen DR1 MOI-0 45 CD14_low


title: THP1_Cas13d_pooledScreen DR1 MOI-0 25 CD11b_high


title: THP1_Cas13d_pooledScreen DR1 MOI-0 25 CD14_low


title: THP1_Cas13d_pooledScreen DR1 MOI-0 45 Day14


title: THP1_Cas13d_pooledScreen wtDR MOI-0 45 Day14


title: THP1_Cas13d_pooledScreen DR1 MOI-0 45 CD14_high


title: THP1_Cas13d_pooledScreen wtDR MOI-0 45 CD14_low


title: THP1_Cas13d_pooledScreen wtDR MOI-0 45 CD11b_high


title: THP1_Cas13d_pooledScreen wtDR MOI-0 25 CD14_high


title: THP1_Cas13d_pooledScreen DR1 MOI-0 25 CD14_high


title: THP1_Cas13d_pooledScreen wtDR MOI-0 45 CD11b_low


title: THP1_Cas13d_pooledScreen wtDR MOI-0 25 CD11b_low


title: THP1_Cas13d_pooledScreen wtDR MOI-0 25 CD11b_high


title: THP1_Cas13d_pooledScreen wtDR MOI-0 45 CD14_high


title: THP1_Cas13d_pooledScreen DR1 MOI-0 25 CD11b_low


title: THP1_Cas13d_pooledScreen DR1 MOI-0 25 Day7


title: THP1_Cas13d_pooledScreen DR1 MOI-0 45 Day7


title: THP1_Cas13d_pooledScreen wtDR MOI-0 45 Day7


title: THP1_Cas13d_pooledScreen wtDR MOI-0 25 Day7


title: KO2

city: Los Angeles

first: Zhengyi

last: Zhang

address: Westwood

institute: UCLA

description: Parkin KO

data_processing:
Raw reads were checked for quality using FastQC, aligned to the Mus musculus GRCm38, and then counted using Mus musculus GRCm38 version 97. Alignment and counting occurred used Rsubread v 2.4.2. Raw counts were then analyzed for differential gene expression using the DESeq2 v1.30.0.
Assembly: GRCm38
Supplementary files format and content: Excel files include differentially expressed genes.

source_name: gonadal white adipose tissue

extract_protocol:
A homogenous portion of frozen adipose samples were homogenized using a tissue homogenizer in Trizol. RNA was isolated using the Qiagen RNeasy Mini QIAcube Kit following the manufacturer’s instructions.
Libraries were prepared using the KAPA mRNA HyperPrep Kit following the manufacturer’s instructions.
The resulting libraries were combined into two pools and sequenced on an Illumina HiSeq 3000 within the UCLA TCGB core facility following in house established protocols.

value: gonadal white adipose tissue

tag: genotype

value: Parkin f/f Adiponectin

tag: treatment

value: High-fat diet


title: THP1_Cas13d_pooledScreen DR1 MOI-0 25 Day14


title: Control5

value: Control f/f


title: KO4

description: Parkin KO


title: KO5

description: Parkin KO


title: KO1

description: Parkin KO


title: THP1_Cas13d_pooledScreen wtDR MOI-0 25 Day14


title: Control4


title: Control3


title: KO3

description: Parkin KO


title: THP1 and HEK293FT cells, GDO-derived cDNA 10x lane 2

description:
guide RNA library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Tag reads
Guide-derived oligonucleotide (GDO)
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO2.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO2.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO2.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GDO.feature_ref.csv.gz

value: GDO


title: THP1 and HEK293FT cells, GDO-derived cDNA 10x lane 4

description:
guide RNA library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Tag reads
Guide-derived oligonucleotide (GDO)
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO4.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO4.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO4.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GDO.feature_ref.csv.gz


title: Control2


title: THP1 and HEK293FT cells, mRNA-derived cDNA 10x lane 4

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO4.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO4.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO4.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz

value: mRNA


title: THP1 and HEK293FT cells, GDO-derived cDNA 10x lane 3

description:
guide RNA library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Tag reads
Guide-derived oligonucleotide (GDO)
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO3.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO3.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO3.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GDO.feature_ref.csv.gz


title: THP1 and HEK293FT cells, HTO-derived cDNA 10x lane 4

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO4.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO4.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO4.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO.feature_ref.csv.gz

molecule: protein

value: HTO

value: anti-B2M (Purified anti-human β2-microglobulin [2M2]), anti-CD298 clone:LNH-94


title: THP1 and HEK293FT cells, HTO-derived cDNA 10x lane 2

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO2.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO2.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO2.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO.feature_ref.csv.gz


title: THP1 and HEK293FT cells, HTO-derived cDNA 10x lane 3

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO3.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO3.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO3.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO.feature_ref.csv.gz


title: THP1 and HEK293FT cells, ADT-derived cDNA 10x lane 1

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT1.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT1.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT1.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT.feature_ref.csv.gz

value: ADT

value: CD9 TotalSeq™-A0579,  CD11a TotalSeq™-A0185,  CD11b TotalSeq™-A0161,  CD11c TotalSeq™-A0053,  CD16 TotalSeq™-A0083,  CD29 TotalSeq™-A0369,  CD33 TotalSeq™-A0052,  CD45RA TotalSeq™-A0063,  CD46 TotalSeq™-A0858,  CD52 TotalSeq™-A0033,  CD55 TotalSeq™-A0383,  CD56 TotalSeq™-A0047,  CD59 TotalSeq™-A0361,  CD63 TotalSeq™-A0404,  CD71 TotalSeq™-A0394,  CD123 TotalSeq™-A0064,  CD127 TotalSeq™-A0390,  CD135 TotalSeq™-A0351,  CD183 TotalSeq™-A0140,  CD185 TotalSeq™-A0144,  HLA-DR TotalSeq™-A0159,  IgM TotalSeq™-A0136


title: THP1 and HEK293FT cells, mRNA-derived cDNA 10x lane 2

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO2.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO2.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO2.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz


title: THP1 and HEK293FT cells, ADT-derived cDNA 10x lane 2

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT2.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT2.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT2.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT.feature_ref.csv.gz


title: THP1 and HEK293FT cells, ADT-derived cDNA 10x lane 4

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT4.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT4.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT4.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT.feature_ref.csv.gz


title: THP1 and HEK293FT cells, mRNA-derived cDNA 10x lane 3

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO3.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO3.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO3.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz


title: THP1 and HEK293FT cells, mRNA-derived cDNA 10x lane 1

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO1.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO1.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO1.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz


title: Control1


title: THP1 and HEK293FT cells, GDO-derived cDNA 10x lane 1

description:
guide RNA library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Tag reads
Guide-derived oligonucleotide (GDO)
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO1.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO1.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GEXGDO1.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.GDO.feature_ref.csv.gz


title: THP1 and HEK293FT cells, HTO-derived cDNA 10x lane 1

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO1.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO1.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO1.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.HTO.feature_ref.csv.gz


title: THP1 and HEK293FT cells, ADT-derived cDNA 10x lane 3

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT3.barcodes.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT3.features.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT3.matrix.mtx.gz
THP1-CaRPool-seq.metadata.tsv.gz
HEK293FTstabRNA.metadata.tsv.gz
THP1-CaRPool-seq_and_HEK293FTstabRNA.ADT.feature_ref.csv.gz


title: I-5402_Day0_R

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

data_processing:
Cell Ranger 3.0.1 (http://10xgenomics.com) was used to process Chromium single cell 5’ RNA-seq output. First, “cellranger mkfastq” demultiplexed the sequencing samples based on the 8bp sample index read to generate fastq files for the Read1 and Read2, followed by extraction of 16bp cell barcode and 10bp UMI. Second, “cellranger count” aligned the Read2 to the human reference genome (GRCh38) using STAR. Then,  aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons without PCR duplicates. Valid cell barcodes were defined based on UMI distribution.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: whole blood

extract_protocol:
For the single cell analysis, cryopreserved PBMCs derived from three responders and three non-responders taken before and 7 days post vaccination were thawed and re-stimulated with the antigen mix as described above for the flow cytometry approach. Subsequently CD45-expressing cells were sorted and subjected loaded onto a well on a 10x Chromium Single Cellinstrument (10x Genomics).
The cDNA libraries were constructed using the 10x Chromium™ Single cell 5’ Library Kit according to the manufacturer’s original protocol. Libraries were sequenced on an Illumina NovaSeq 6000 2x50 paired-end kits using the following read length: 26 bp Read1 for cell barcode and UMI, 8 bp I7 index for sample index  and 89 bp Read2 for transcript.

value: whole blood

value: PBMC

tag: phenotype

value: R

tag: donor


title: I-5127_Day0_R


title: I-5127_Day7_R


title: I-4964_Day0_NR

value: NR


title: I-4236_Day7_NR


title: I-4964_Day7_NR


title: I-4229_Day7_R


title: I-4236_Day0_NR


title: I-4229_Day0_R


title: I-0845_Day7_NR


title: I-0845_Day0_NR


title: I-5402_Day7_R


title: HI47P404882

data_processing:
RTA 3.4.4, bcl2fastq 2.20.0.422 (Illumina)
Before alignment to reference genome each sequence in the raw FASTQ files were trimmed on base call quality and sequencing adapter contamination using Trim Galore! wrapper tool. Reads shorter than 20 bp were removed from FASTQ file. Trimmed reads were aligned to the reference genome using open source short read aligner STAR (https://code.google.com/p/rna-star/) with settings according to log file. Feature counts were determined using R package “Rsubread”. Only genes showing counts greater 5 at least two times across all samples were considered for further analysis (data cleansing). Gene annotation was done by R package “bioMaRt. Before starting the statistical analysis steps,  expression data was log2 transformed and TMM normalized (edgeR).
Assembly: hg38
Supplementary files format and content: Matrix table with TMM-normalizedl log2CPM for every gene and every sample

source_name: Lymphoycyte

extract_protocol:
The “PAXgene Blood miRNA Kit” (Qiagen) was used for the purification of miRNA  and total RNA.
100ng total RNA was depleted for rRNA and globin by using QIAseq® FastSelectTM RNA Removal Kit (Qiagen). The RNA Sequencing library was prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs). The libraries were sequenced on Illumina NovaSeq6000 using NovaSeq6000 S2 Reagent Kit (100 cycles, paired ended run) with an average of 50 Mio reads per RNA sample.

value: Lymphoycyte

value: TR


title: HI47P101314


title: HI47P506007


title: HI47P403810


title: HI47P501354


title: HI47P103826


title: HI47P803652


title: HI47P701211


title: HI47P503677


title: HI47P200785


title: HI47P902780


title: HI47P001458


title: HI47P504883


title: HI47P504874


title: HI47P801294


title: HI47P303800


title: Mesenchymal stem cell, ankylosing spondylitis patient 1,induction day 10

city: Guangzhou

first: Zhenhua

last: Liu

state: Guangdong

address: industry Avenue 253#

department: Spine surgery

institute: Zhujiang Hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The remaining reads were filtered against the rRNA database to remove possible ribosomal RNA contamination,  and then mapped to the hg19 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM/counts for each Sample

source_name: Bone marrow

growth_protocol: mesenchymal stem cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from MSCs using the Trizol (invitrogen) according to the manufacturer’s instructions
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit according to instructions.

treatment_protocol: Adipogenic differentiation was induced for 10 days with 0.2 mM indomethacin (Sigma–Aldrich), 10 μg/mL insulin (Sigma–Aldrich), 0.5 mM 3-isobutyl-1-methylxanthine (Sigma–Aldrich) and 1 μM dexamethasone(Sigma–Aldrich)

value: Bone marrow

value: mesenchymal stem cells

value: WT

value: adipogenic differentiation

tag: disease state

value: ankylosing spondylitis


title: Mesenchymal stem cell, ankylosing spondylitis patient 2,induction day 10


title: Mesenchymal stem cell, healthy donor 1,induction day 10

value: healthy


title: Mesenchymal stem cell, ankylosing spondylitis patient 3,induction day 10


title: HI47P901457


title: HI47P902717


title: HI47P206004


title: Mesenchymal stem cell, healthy donor 2,induction day 10


title: HI47P402712


title: HI47P003870


title: Mesenchymal stem cell, healthy donor 3,induction day 10


title: HI47P203764


title: He78

city: San Diego

first: Ashu

last: Sethi

address: 9420 Athena Circle

department: Health Sciences

institute: La Jolla Institute for Immunology

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the mm10 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Assembly: GRCh38.gencode.v27B
Supplementary files format and content: read count matrix with rows as genes and columns as cells

source_name: Donor 3

growth_protocol: Cells grown and plated for experiments in smooth muscle cell medium supplemented with 2% FBS, 1% SMGS, 100u/ml penicilin and 100ug/ml streptomicin (ScienCell, CA)

extract_protocol:
Qiagen miRNeasy Micro Kit (Qiagen 217084)
200ng RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB E7490L) prior to NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB E7760L)

treatment_protocol: Cells pre-starved to serum/growth factor free smooth muscle cell medium with 100u/ml penicilin and 100ug/ml streptomicin. After 16 hours pre-starvation, cells were treated with the specified doses of cytokine diluted on starvation medium, for 24 hours

value: Esophagus

value: Fibroblast

tag: agent


title: He97

source_name: Donor 4


title: HI47P703732


title: JUNB, rep2

city: Valencia

first: Rosa

last: Farràs

state: Valencia

address: Eduardo Primo Yúfera, 12

institute: Centro de Investigación Príncipe Felipe

description:
UTD6 I 9 11b
macs14_UTD6_I_9_11b_vs_UTD6_input_9_11b_model-s_peaks.bed
macs14_UTA6_finalcommonpeaks.bed

data_processing:
Reads were aligned to the human genome (hg19) using CASAVA (Illumina)
Peak calling was performed using MACS2 and p-value cutoff 1.00e-05, setting as control the input samples.
Only peaks found across biological replicates (BEDtools (Quinlan, A.R. and I.M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 2010. 26(6): p. 841-2.)), 1 bp minimum overlapping, were considered as binding sites for downstream analysis. BED files from biological replicates were merged.
Genome_build: Hg19
Supplementary_files_format_and_content: bed

source_name: U2OS cells

growth_protocol: U20S-derived UTA6 cells  (Englert C, Hou X, Maheswaran S, Bennett P, Ngwu C, Re G G, Garvin A J, Rosner M R, Haber D A. WT1 suppresses synthesis of the epidermal factor receptor and induces apoptosis. EMBO J. 1995;14:4662–4675) were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal calf serum and penicillin/streptomycin (100µg/ml each) in a humidified 5% CO2 atmosphere at 37°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and JUNB complexes were isolated with the appropriate antibodies.
ChIP-seq libraries were prepared using the TruSeq ChIP sample reparation kit from Illumina by the MGX sequencing Platform (Montpellier, France)  ChIP-seq - Instrument model : Illumina HiSeq 2500 (MGX Platform, Montpellier France).

treatment_protocol: experiments were carried out in 2 independent replicates for JUNB and input

tag: cell line

value: U2OS-derived UTA6 cells

value: osteosarcoma cell

tag: clone

value: U2OS-derived UTA6 clone

tag: chip antibody

value: JUNB (Cell Signaling (#3753))

value: untreated


title: HI47P501453

tag: tissue

value: PBMC

tag: time


title: KLM03_Tr_LN_SAH-FOXP3(229-259)C

city: Chicago

first: James

last: LaBelle

state: IL

address: 900 East 57th Street, KCBD 5122

institute: University of Chicago

description:
cpm.KLM03
LaBelle_GEO_ProcessedData_Treg.txt

data_processing:
Sequence reads were mapped to mm10 using Tophat and Bowtie using default parameters.
Differential expression analysis was performed using EdgeR
Data was filtered to exclude genes with cpm <2 in 3 or more samples
Assembly: mm10
Supplementary files format and content: tab-delimited text files include cpmvalues for each sample

source_name: Lymph Node

extract_protocol:
RNA was isolated using Trizol and harvested using the Zymo Research Direct-zol RNA Miniprep kit. 1ug of RNA was used for library construction.
RNA-seq libraries were generated using an Illumina TruSEQ stranded mRNA library prep kit (following the manufacturer’s protocol)

treatment_protocol: Mice were treated once per day for two days with either vehicle or 25mg/kg SAH-FOXP3(229-259)C delivered through intraperitoneal injection

value: Lymph Node

value: naive primary T cell

tag: cell type

value: CD4+CD25+FOXP3+ Treg

value: B6.Cg-Foxp3tm2Tch/J (FOXP3-IRES-GFP)


title: He100

source_name: Donor 1


title: HI47P100766

value: Lymphoycyte

value: TR


title: HI47P400750


title: HI47P103754


title: He109

source_name: Donor 2


title: KLM06_Tr_SPL_SAH-FOXP3(229-259)C

description:
cpm.KLM06
LaBelle_GEO_ProcessedData_Treg.txt

source_name: Spleen

value: Spleen


title: JUNB, rep1

description:
UTD6 I 10 11a
macs14_UTD6_I_10_11a_vs_UTD6_input_10_11a_model-s_peaks.bed
macs14_UTA6_finalcommonpeaks.bed


title: HI47P201351


title: Input, rep1

description:
UTD6 input 10 11a
macs14_UTD6_I_10_11a_vs_UTD6_input_10_11a_model-s_peaks.bed


title: HI47P002736


title: HI47P301253


title: KLM01_Tr_LN_DMSO

description:
cpm.KLM01
LaBelle_GEO_ProcessedData_Treg.txt

value: Vehicle


title: KLM04_Tr_SPL_DMSO

description:
cpm.KLM04
LaBelle_GEO_ProcessedData_Treg.txt


title: Input, rep2

description:
UTD6 input 9 11b
macs14_UTD6_I_9_11b_vs_UTD6_input_9_11b_model-s_peaks.bed


title: KLM05-Tr_SPL_SAH-FOXP3(229-259)C

description:
cpm.KLM05
LaBelle_GEO_ProcessedData_Treg.txt


title: KLM06_Tc_SPL_SAH-FOXP3(229-259)C

description:
cpm.KLM06
LaBelle_GEO_ProcessedData_Tcon.txt

value: CD4+ Tcon


title: KLM02_Tr_LN_SAH-FOXP3(229-259)C

description:
cpm.KLM02
LaBelle_GEO_ProcessedData_Treg.txt


title: KLM03_Tc_LN_SAH-FOXP3(229-259)C

description:
cpm.KLM03
LaBelle_GEO_ProcessedData_Tcon.txt


title: KLM02_Tc_LN_SAH-FOXP3(229-259)C

description:
cpm.KLM02
LaBelle_GEO_ProcessedData_Tcon.txt


title: HiC__limb_HH25_wt_chicken_Rep-1

city: Berlin

first: Michael

middle: I

last: Robson

address: Max Planck Institut für molekulare Genet, Ihnestrasse 63-73

institute: Max Planck Institute for Molecular Genetics

data_processing:
Fastq files were processed with the Juicer pipeline v1.5.6 (Durand et al., 2016) (CPU version) using bwa v0.7.17 (Li and Durbin, 2010) for mapping short reads to the reference genomes mm10 (mouse), hg19 (human), galGal6 (chicken), monDom5 (opossum), susScr11.1 (pig), and AmexG_v6.0-DD (axolotl), respectively.
Replicates were merged after the mapping, filtering and deduplication steps of the Juicer pipeline. Juicer tools v1.7.5 (Durand et al., 2016) were used to generate binned and KR normalized HiC maps from read pairs with MAPQ≥30.
For compartment analysis, hic-files were converted at 100kb bin size to the cool format using hic2cool (v0.8.2) (https://github.com/4dn-dcic/hic2cool) and balanced using cooler (v0.8.5) (Abdennur and Mirny, 2020). Afterwards, compartment analysis was performed using cooltools (v0.3.0) (https://github.com/open2c/cooltools) and using the GC content as reference track.  TADs were identified by applying TopDom v.0.0.228 on 50-kb binned and KR-normalized maps using a window size of 10 (Shin et al., 2016).
Genome_build: mondom5 and galgal6
Supplementary_files_format_and_content: .hic

organism: Gallus gallus

source_name: limb

growth_protocol: Embryonic limb cells were isolated from chicken or opossum embryos through limb dissection, trypsinization, filtration (100 µm) and centrifugation.

extract_protocol: A S-Series 220 Covaris was used to shear the DNA to fragments of 300–600 bp for library preparation, and biotin-filled DNA fragments were pulled down using Dynabeads MyOne Streptavidin T1 beads. DNA ends were subsequently repaired using T4 DNA polymerase and the Klenow fragment of DNA polymerase I and phosphorylated with T4 Polynucleotide Kinase NK. DNA was further prepared for sequencing by ligating adaptors to DNA fragments, using the NEBNext Multiplex Oligos for Illumina kit. Indexes were added via PCR amplification (4–8 cycles) using the NEBNext Ultra II Q5 Master Mix. PCR purification and size selection were carried out using Agencourt AMPure XP beads. Libraries were sequenced on a x platform yielding x bp paired-end reads. For each sample, the HiC library was created by pooling a total of four technical replicates generated from two different cell isolations cultures in order to ensure higher complexity of the sequencing library

treatment_protocol: HiC libraries were prepared as described in a previously published in situ protocol (Melo et al., 2020; Rao et al., 2014). Briefly, ∼1 million cells were fixed in 2% formaldehyde, lysed, and stored at -80°C.

tag: Stage

value: wt


title: KLM05-Tc_SPL_SAH-FOXP3(229-259)C

description:
cpm.KLM05
LaBelle_GEO_ProcessedData_Tcon.txt


title: KLM01_Tc_LN_DMSO

description:
cpm.KLM01
LaBelle_GEO_ProcessedData_Tcon.txt


title: DamID-seq_Dam-LMNB1_limb_E115_wt_mouse_Rep-1

data_processing:
Library strategy: DamID-seq
Raw reads from DamID-seq experiments were mapped to the mouse mm10 reference genome using the alignment tool BWA-MEM (v.0.7.12) (Li and Durbin, 2009).
The counts of mapped reads overlapping a DpnII (GATC) restriction fragment side were normalized by reads per kilobase, divided by the length of the fragment, per million mapped reads (RPKM).
Based on these normalized counts the log2 fold change between the Dam–Lamin B1 transduced samples and the respective Dam-only-encoding samples was calculated.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files of log2 ratios of Dam-LMNB1/Damonly signal.

growth_protocol: Mouse G4 ESCs (XY, 129S6/SvEvTac x C57BL/6Ncr F1 hybrid) were grown as described previously on a mitomycin-inactivated CD1 mouse embryonic fibroblast feeder monolayer on gelatinised dishes  at 37oC, 7.5% CO2 (Andrey and Spielmann, 2017; George et al., 2007). ESCs were cultured in ESC medium containing knockout DMEM with 4,5 mg/ml glucose and sodium pyruvate supplemented with 15% FCS, 10 mM Glutamine, 1x penicillin/streptomycin, 1x non-essential amino acids, 1x nucleosides, 0.1 mM beta-Mercaptoethanol and 1000 U/ml LIF. Medium was changed every day while G4-cells were split every 2-3 days or were frozen at 1x 106 cells/cryovial in ESC medium containing 20% FCS and 10% DMSO. ESCs and feeder cells were tested for Mycoplasma contamination using the MycoAlert detection kit and MycoAlert Assay Control Set.    E11.5 forelimb cells were isolated from C57BL/6 embryonic limbs through trypsinization, filtration (100 µm) and centrifugation. When cultured in vitro, forelimb cells were grown on gelatine-coated plates at 37oC in 7.5% CO2 for up to 48 h in limb medium (DMEM/F12, 10% FCS, 1% penicillin/streptomycin, 4 mM L-Glutamine) supplemented with 250 ng/ml Recombinant Mouse Wnt-3a protein and 150 ng/ml Recombinant Human/Mouse FGF-8b Isoform.

extract_protocol:
DNA  was  extracted  from  cells  using  the  DNeasy  tissue  lysis  kit  as  per  manufacturer’s  instructions.
DamID  sample  processing  was  then  performed  as  described previously (Robson and Schirmer, 2016).  Briefly,   2.5  μg  of  extracted  DNA  was  then  digested by DpnI and, following heat inactivation of DpnI,  was ligated to the DamID adaptor duplex (dsAdR) generated from the oligonucleotides AdRt (5’-CTAATACGACTCACATAGGGCAGCGTGGTCGCGGCCGA-GGA-3’)  and AdRb (5’-TCCTCGGCCG-3’) after which DNA was further digested by DpnII. To amplify DNA sequences methylated by the Dam methylase, 5 μl of DpnII digested material was then subjected to PCR in the supplied buffer in the presence of the 1.25 μM Adr-PCR primer (5’-GGTCGCGGCCGAGGATC-3’), 0.2 mM dNTPs and 1X of the Advantage cDNA polymerase. PCR was performed as previously described after which amplified DNA was purified, processed into NGS libraries using the KAPA HyperPrep kit and analyzed for quality by Bioanalyzer analysis.  standard protocols. DamID-seq samples were sequenced 75 or 100 bp paired-end reads and each experiment was performed in duplicates for sequencing.

treatment_protocol: DamID was performed as described previously (Robson and Schirmer, 2016). Briefly, lentiviruses encoding the Dam methylase alone (pLgw V5-EcoDam) or fused to lamin B1 (pLgw-EcoDam-V5-Lamin) were  generated in 293FT cells. Here, ~6 million 293FT cells were transfected with 2.8  μg  pMD2.G,  4.6  μg  psPAX2, and  7.5  μg  of  pLgw V5-EcoDam or pLgw-EcoDam-V5-Lamin with 36 μl lipofectamine 2000 in 3 ml Optimem. After 16 h, 293FT media was replaced. Virus-containing supernatants were subsequently aspirated after 48 h and 72 h. Viral supernatants were then cleared of cellular debris by 10 min centrifugation at 3,500 rpm and subsequent filtration through a 0.45 μm2 low protein-binding PES syringe filter. Viral supernatants were finally purified using the Lent-X concentrator as per manufacturer's instructions and resuspended in Optimem. If  not  used  immediately,  aliquots  were  frozen  at  -80°C.    To perform DamID, ESCs and cultured E11.5 limb cells were transduced with DamID lentiviruses and harvested 72 or 48 h later, respectively. Specifically, 1,5x105 ESCs were plated feeder-free onto gelatinized 6 well 1 h prior to transduction with DamID lentiviruses. Transduction was then performed overnight after which virus-containing media was removed and cells were plated with feeders in 6 cm plates. After 48 h, contaminating feeders were removed by further feeder-depletion and pure ESCs were isolated by centrifugation. By contrast, isolated E11.5 limb bud cells were directly plated and transduced after 1 h. Virus-containing media was removed 24 h later after which cells were isolated after an additional 48 h.

tag: cell-type/stage

tag: damid condition


title: HI47P701428


title: KLM04_Tc_SPL_DMSO

description:
cpm.KLM04
LaBelle_GEO_ProcessedData_Tcon.txt


title: DamID-seq_Damonly_limb_E115_wt_mouse_Rep-1

value: Damonly


title: DamID-seq_Damonly_limb_E115_wt_mouse_Rep-2


title: HI47P701329


title: DamID-seq_Dam-LMNB1_limb_E115_wt_mouse_Rep-2


title: HI47P602741


title: HI47P501219


title: DamID-seq_Dam-LMNB1_ESC_G4_wt_mouse_Rep-1

source_name: ESC

value: XY, 129S6/SvEvTac x C57BL/6Ncr F1 hybrid


title: DamID-seq_Dam-LMNB1_ESC_G4_wt_mouse_Rep-2


title: DamID-seq_Damonly_ESC_G4_wt_mouse_Rep-4


title: HEK293FT and Mouse NIH/3T3 cells, GDO-derived cDNA

description:
guide RNA library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Tag reads
Guide-derived oligonucleotide (GDO)
HEK293FT_and_SpeciesMixing_CaRPool-seq.GEXGDO.barcodes.tsv.gz
HEK293FT_and_SpeciesMixing_CaRPool-seq.GEXGDO.features.tsv.gz
HEK293FT_and_SpeciesMixing_CaRPool-seq.GEXGDO.matrix.mtx.gz
HEK293FT_CaRPool-seq.metadata.tsv.gz
SpeciesMixing_CaRPool-seq.metadata.tsv.gz
HEK293FT_and_SpeciesMixing_CaRPool-seq.GDO.feature_ref.csv.gz

organism:
Homo sapiens
Mus musculus

source_name: kidney, fibroblast

value: kidney, fibroblast

value: epithelial embryonic kidney cells, mouse fibroblast

tag: library type

value: GDO


title: DamID-seq_Damonly_ESC_G4_wt_mouse_Rep-1


title: DamID-seq_Damonly_ESC_G4_wt_mouse_Rep-3


title: DamID-seq_Dam-LMNB1_ESC_G4_wt_mouse_Rep-3


title: DamID_Damonly_ESC_G4_E35_mm10_dRex1_dTrim

data_processing:
Raw reads from DamID-seq experiments were mapped to the mouse mm10 reference genome using the alignment tool BWA-MEM (v.0.7.12) (Li and Durbin, 2009).
The counts of mapped reads overlapping a DpnII (GATC) restriction fragment side were normalized by reads per kilobase, divided by the length of the fragment, per million mapped reads (RPKM).
Based on these normalized counts the log2 fold change between the Dam–Lamin B1 transduced samples and the respective Dam-only-encoding samples was calculated.
Assembly: mm10
Supplementary files format and content: bigwig files of log2 ratios of Dam-LMNB1/Damonly signal.
Library strategy: DamID-seq

value: ESC


title: DamID-seq_Damonly_ESC_G4_wt_mouse_Rep-2


title: HI47P600239

value: PBMC


title: DamID_LMNB1_ESC_G4_E35_mm10_dRex1


title: DamID_LMNB1_ESC_G4_E35_mm10_dRex1_dTrim


title: HI47P603786


title: DamID_Damonly_ESC_G4_E35_mm10_dRex1


title: HEK293FT and Mouse NIH/3T3 cells, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
HEK293FT_and_SpeciesMixing_CaRPool-seq.HTO.barcodes.tsv.gz
HEK293FT_and_SpeciesMixing_CaRPool-seq.HTO.features.tsv.gz
HEK293FT_and_SpeciesMixing_CaRPool-seq.HTO.matrix.mtx.gz
HEK293FT_CaRPool-seq.metadata.tsv.gz
SpeciesMixing_CaRPool-seq.metadata.tsv.gz
HEK293FT_and_SpeciesMixing_CaRPool-seq.HTO.feature_ref.csv.gz

value: HTO

tag: antibodies/tags

value: HTO_01 TotalSeq™-A0251,  HTO_02 TotalSeq™-A0252,  HTO_03 TotalSeq™-A0253,  HTO_04 TotalSeq™-A0254,  HTO_05 TotalSeq™-A0255,  HTO_06 TotalSeq™-A0256,  HTO_07 TotalSeq™-A0257,  HTO_08 TotalSeq™-A0258,  HTO_10 TotalSeq™-A0260


title: HI47P403757


title: HI47P401380


title: HI47P100720


title: DamID-seq_Dam-LMNB1_ESC_G4_wt_mouse_Rep-4

tag: genotype


title: HEK293FT and Mouse NIH/3T3 cells, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
HEK293FT_and_SpeciesMixing_CaRPool-seq.GEXGDO.barcodes.tsv.gz
HEK293FT_and_SpeciesMixing_CaRPool-seq.GEXGDO.features.tsv.gz
HEK293FT_and_SpeciesMixing_CaRPool-seq.GEXGDO.matrix.mtx.gz
HEK293FT_CaRPool-seq.metadata.tsv.gz
SpeciesMixing_CaRPool-seq.metadata.tsv.gz

value: mRNA


title: HEK293FT and Mouse NIH/3T3 cells, ADT-derived cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
HEK293FT_and_SpeciesMixing_CaRPool-seq.ADT.barcodes.tsv.gz
HEK293FT_and_SpeciesMixing_CaRPool-seq.ADT.features.tsv.gz
HEK293FT_and_SpeciesMixing_CaRPool-seq.ADT.matrix.mtx.gz
HEK293FT_CaRPool-seq.metadata.tsv.gz
SpeciesMixing_CaRPool-seq.metadata.tsv.gz
HEK293FT_and_SpeciesMixing_CaRPool-seq.ADT.feature_ref.csv.gz

value: ADT

value: CD46 TotalSeq™-A0858,   CD55 TotalSeq™-A0383,  CD71 TotalSeq™-A0394,  CD29 TotalSeq™-A0369,  CD56 TotalSeq™-A0047


title: HI47P401263

value: Lymphoycyte

value: TR


title: HI47P902744


title: HiC__limb_stage30_wt_opossum_Rep-2

organism: Monodelphis domestica


title: Neutro Spleen Cxcr2-/- Rep4

city: Montpellier

first: Gwendal

last: LAZENNEC

address: 1682 rue de la Valsiere

country: France

institute: CNRS

data_processing:
Raw sequencing data was quality-controlled with the FastQC program. Low quality reads were trimmed or removed using Trimmer (minimum length: 120 bp).
Reads were aligned to the mouse reference genome (mm10 build) with the Star tool.
Gene counts were obtained by read counting software Htseq.
Assembly: mm10
Supplementary files format and content: txt files

extract_protocol:
Neutrophils were purified by flow cytometry, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: age

value: 10 weeks

tag: housing

value: SOPF

value: Spleen


title: HI47P903789

tag: phenotype

tag: donor


title: HI47P703822


title: Neutro Spleen Cxcr2-/- Rep1


title: Neutro Spleen Cxcr2-/- Rep3


title: HI47P801302


title: Neutro Spleen Cxcr2-/- Rep2


title: HI47P701455


title: HI47P000710


title: Neutro Spleen  WT Rep1

value: FVB-WT

value: WT


title: HiC__limb_stage30_wt_opossum_Rep-1

value: wt


title: Overexpression11

description: Nqo1 overexpression

value: gonadal white adipose tissue

tag: treatment

value: High-fat diet


title: Neutro Spleen  WT Rep4


title: Neutro Spleen  WT Rep2


title: Neutro Spleen  WT Rep3


title: HI47P101233


title: TLRB, replicate 2, scRNAseq

city: Boston

last: Markmann

state: MA

address: 55 Fruit St., WHT 517

institute: Massachusetts General Hospital

description: 10x Genomics

data_processing:
Fastq files were de-multiplexed using Illumina bcl2fastq, followed by alignment, filtering, barcode counting, and UMI counting using CellRanger version 3.1.0. As a reference, mouse mm10 (Ensembl 93) version 3.0.0 and CellRanger aggr were used to combine and normalize Gelbeads-in-Emulsion (GEM) wells.
Assembly: mouse mm10 (Ensembl 93) version 3.0.0
Supplementary files format and content: Fastq files

extract_protocol: An estimated 5,000 cells were used for GEM generation and libraries were prepared using the recommended protocol (Chromium Single Cell 3ʹ v3).

tag: cell line

value: B cells

value: Splenocyte

value: Bregs-TLR were generated on Bregs-CpG by adding LPS, PMA, and ionomycin on the final day, for 5 hours before collection.


title: CpGB, replicate 2, scRNAseq

description: 10x Genomics

value: Bregs-CpG were produced by culturing purified B cells in Complete Medium with CpG B ODN 1668 for 3 days


title: TLRB, replicate 1, scRNAseq

description: 10x Genomics


title: HI47P001368

value: PBMC


title: CpGB, replicate 1, scRNAseq

description: 10x Genomics


title: HI47P400228


title: Overexpression10

description: Nqo1 overexpression


title: HI47P000288


title: Overexpression12

description: Nqo1 overexpression


title: HI47P304863

value: TNR


title: HI47P701365


title: HI47P703688


title: Overexpression9

description: Nqo1 overexpression


title: HI47P302784


title: Differentiating cells, Ino80 iKO ESCs

city: Seoul

first: Kwonho

last: Hong

address: 120 Neungdong

country: South Korea

institute: Konkuk university

data_processing:
Reads were mapped to the mm10 UCSC Mus musculus genome using the STAR (v2.7.9a).
Mapped reads were quantified and normalized to FPKM values using the Cuffquant and Cuffnorm tools of the Cufflinks (v2.2.1) toolset.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: differentiating ESC

growth_protocol: For EBs formation, ESCs were induced to the primed state in serum-medium for two days. Then, 500,000 ESCs were suspended in 5 mL KSR medium [Dulbecco's Modified Essential Medium (DMEM) (Hyclone) supplemented with 8% KSR (Gibco), penicillin/streptomycin (Gibco), and β-mercaptoethanol (Gibco)] to allow them to form EBs. The EBs were fed every 2 days. At day 4 of EBs formation, the EBs were transferred to a 0.2% gelatin-coated culture dish containing KSR medium and allowed to attach. The following day, EBs were fed with differentiation medium [DMEM (Hyclone) supplemented with 15% FBS( Welgene), Minimum Essential Medium (MEM) non-essential amino acids (Gibco), penicillin/streptomycin (Gibco), sodium pyruvate, β-mercaptoethanol (Gibco), and BMP4 (R&D Systems)] with 0.5uM 4-OHTM (Sigma), and cultured for 7 days.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeqStranded mRNA Sample Preparation Kit following manufacturer's protocols.

value: differentiating ESC

value: Ino80 knockout


title: Differentiating cells, Control ESCs


title: Control12

value: AAV8 Control


title: Control11


title: LP line age control biol rep 3 [LP_C3]

city: Philadelphia

first: Abigail

last: DiVito Evans

state: Pennsylvania

address: 433 S University Ave, 205 Carolyn Lynch Lab

department: Biology

institute: University of Pennsylvania

description:
LP_C3.bam
HP_LP_featurecounts.txt

data_processing:
Sequence reads were trimmed for adaptor and low quality sequences using Trimmomatic
Trimmed reads were mapped to the Drosophila melanogaster genome version r6.42 from flybase.org using STAR alignment
Raw count data was generated using featureCounts from read alignments
Differential expression was analyzed using DESeq2 in R
Assembly: r6.24 from flybase.org
Supplementary files format and content: tab-delimited text file includes a matrix of count data for all samples in this experiment

organism: Drosophila melanogaster

source_name: Ovary stages 1-7

extract_protocol:
Total mRNA was extracted using Mirvana miRNA isolation kit
Libraries were constructed using the NEBNext Ultra II Directional protocol with PolyA selection

value: Ovary stages 1-7

value: WT "LP" line

value: 28 days old at 25C


title: LP line age control biol rep 1 [LP_C1]

description:
LP_C1.bam
HP_LP_featurecounts.txt


title: LP line reproductive biol rep 3  [LP_R3]

description:
LP_R3.bam
HP_LP_featurecounts.txt

value: persistently reproductive at 12C


title: HI47P302711

value: Lymphoycyte


title: LP line age control biol rep 2 [LP_C2]

description:
LP_C2.bam
HP_LP_featurecounts.txt


title: LP line reproductive biol rep 2  [LP_R2]

description:
LP_R2.bam
HP_LP_featurecounts.txt


title: HI47P202792


title: RT3

city: Stanford

first: Yoko

last: Nishiga

address: 265 Campus Drive

department: Departments of Pediatrics and Genetics

institute: Stanford University

data_processing:
RNA qunatification done by salmon version 0.8.2
Differential expression analysis with DESeq2 version 1.22.2
Genome_build: mm10
Supplementary_files_format_and_content: quant.sf files are tab delimited text files

source_name: Cell line KP1

growth_protocol: KP1 cells were cultured in RPMI-1640 medium supplemented with 10% bovine growth serum and 1% penicillin-streptomycin-glutamine.

extract_protocol:
RNA was harvested using RNAeasy Mini Kit.
Library preparation and sequencing were performed by Novogene using Illumina’s sequencing platform.

treatment_protocol: The cell pellets were collected 24 hours after 5Gy radiation.

tag: cancer type

value: small cell lung cancer

value: irradiated


title: HI47P103691

tag: tissue


title: Control9

source_name: gonadal white adipose tissue

value: gonadal white adipose tissue

value: High-fat diet


title: BLM_HBO_3

city: Southampton

first: Yihua

last: Wang

address: University Road

institute: University of Southampton

description: Six to eight weeks old male C57BL/6 mice (20-25 g) after bleomycin instillation were randomly divided into bleomycin (BLM) group and BLM+HBO group in day 7 post bleomycin instillation. Then mice in BLM+HBO group were exposed to repetitive HBO treatment (2.5 ATA, 90 min/time/day) for 14 consecutive days, while the mice in the BLM group were placed in the chamber for the same duration without pure oxygen pressurization. The lung tissues were collected at day 21. RNA-seq based on next generation sequencing was applied with 4 samples in bleomycin group and 3 samples in bleomycin + HBO group.

data_processing:
Illumina NovaSeq 6000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus musculus genome Ensembl GRCm38 using Hisat2 v2.2.0 with default parameters
Raw counts were calculated by featureCounts (version 2.2.0) with default parameters
Assembly: Mus musculus genome Ensembl GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

extract_protocol:
Trizol, following the manufacturer instruction
NEBNext® UltraTM RNA Library Prep Kit, following the manufacturer instruction

value: Lung

tag: Sex

value: male


title: C3

value: untreated


title: LP line reproductive biol rep 1  [LP_R1]

description:
LP_R1.bam
HP_LP_featurecounts.txt


title: HI47P002772

source_name: Lymphoycyte

tag: cell type

value: PBMC

tag: time


title: BLM_HBO_2


title: RT1


title: Control10


title: LP line diapause biol rep 3 [LP_D3]

description:
LP_D3.bam
HP_LP_featurecounts.txt

value: diapause at 12C


title: LP line diapause biol rep 2 [LP_D2]

description:
LP_D2.bam
HP_LP_featurecounts.txt


title: LP line diapause biol rep 1 [LP_D1]

description:
LP_D1.bam
HP_LP_featurecounts.txt


title: HI47P002745

value: TNR


title: BLM_HBO_1


title: HI47P900728


title: HP line age control biol rep 3 [HP_C3]

description:
HP_C3.bam
HP_LP_featurecounts.txt

value: WT "HP" line


title: BLM_4


title: HI47P002709


title: C2


title: BLM_3


title: scRNA-Seq of mouse trachea basal cells (WY001)

city: Tucson

first: Hongxu

last: Ding

state: AZ

address: The University of Arizona

institute: University of Arizona

data_processing:
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt)
R2 read: contains the RNA sequence.
Demultiplexing, alignment, mapping and UMI (Unique Molecular Identifier) quantification were performed using 10x Genomics Cell Ranger pipeline (v2.1.1).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes UMI (Unique Molecular Identifier) counts for each cell.

source_name: Trachea basal cells

extract_protocol:
Standard 10x Genomics scRNA-Seq 3' V2 protocol (CG00052).
Standard Illumina HiSeq 4000 protocol.

treatment_protocol: Adult p63-CreERT2; Rosa26-tdTomato mice were given 240 μg/g body weight TM once via oral gavage. A short chase period of 3 days was used to ensure accumulation of tdTomato in BCs and to minimize tdTomato labeling in luminal descendants. Tracheal BCs were isolated and sorted by DAPI- Lin- EpCAM+ CD104hi tdTomato+.

tag: background strain

value: Mixed from FVB and C57BL6

tag: developmental stage

value: Adult

tag: genetic modification

value: p63-CreERT2; Rosa26-tdTomato

value: Trachea basal cells


title: BLM_2


title: RT2


title: BLM_1


title: HI47P802752


title: HI47P801483


title: HP line age control biol rep 1 [HP_C1]

description:
HP_C1.bam
HP_LP_featurecounts.txt

value: Ovary stages 1-7

value: 28 days old at 25C


title: HP line reproductive biol rep 3  [HP_R3]

description:
HP_R3.bam
HP_LP_featurecounts.txt

value: persistently reproductive at 12C


title: RT+antiCD47_Tumor_1

data_processing:
Sequenced reads were demultiplxed and aligned to the mm10 genome using CellRanger 6.0 software
The cell count matrix was generated using CellRanger count function.
The output matrices of replicates corrsponding to the same treatment were aggregated using the Cellranger aggr function with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: The processed files are folders containing the following three files:aggregated_treatment_barcodes.tsv.gz, aggregated_treatment_features.tsv.gz and aggregated_treatment_matrix.mtx.gz

source_name: CD45+ leukocytes

growth_protocol: KP1 cells were subcutaneously transplanted in the right and left flank of NSG mice.

extract_protocol:
6 days after start of treatment, tumors were collected from the non-irradiated site (left flank) of 3 mice belonging to each treatment group. The tumors were dissociated into single cells and leukocytes were isolated by FACS sorting for CD45+ cells.
Library was constructed using the Chromium Single Cell 3' Reagent Kit (V2 chemistry)

treatment_protocol: 7 days after sub-cutaneous injection, tumors on the right flank of the NSG mice were either treated with radiotherapy (RT) or radiotherapy+antiCD47 antibody.

value: radiotherapy + anti-CD47

value: NSG mice


title: RT+antiCD47_Tumor_3


title: RT_Tumor_3

value: radiotherapy


title: HI47P501426

value: Lymphoycyte


title: RT+antiCD47_Tumor_2


title: HP line reproductive biol rep 1  [HP_R1]

description:
HP_R1.bam
HP_LP_featurecounts.txt


title: HI47P700753


title: HP line diapause biol rep 3 [HP_D3]

description:
HP_D3.bam
HP_LP_featurecounts.txt


title: HI47P500238


title: HP line age control biol rep 2 [HP_C2]

description:
HP_C2.bam
HP_LP_featurecounts.txt


title: HP line diapause biol rep 1 [HP_D1]

description:
HP_D1.bam
HP_LP_featurecounts.txt


title: HP line diapause biol rep 2 [HP_D2]

description:
HP_D2.bam
HP_LP_featurecounts.txt


title: RT_Tumor_1


title: HI47P302757


title: HP line reproductive biol rep 2  [HP_R2]

description:
HP_R2.bam
HP_LP_featurecounts.txt


title: HI47P201261


title: HI47P503811


title: THP1_Cas13d_combinatorial_pooledScreen CD11b_high 300ul_Virus

description:
guide RNA library: read1 file contains barcode (bcgRNA) sequence
barcode guide RNA sequence
none
THP1_Cas13d_combinatorial_pooledScreen.counts.csv.gz

data_processing:
Sequencing reads coming from the mRNA library were mapped to a joined genome reference of hg38 (ensemble v97) and mm10 using the Cellranger Software (v3.0.1), or to hg38 using Cellranger v6.0.0 for the THP1 experiment. Barcode guide RNA library reads were mapped simultaneously to a barcode reference using Cellranger. To generate count matrices for HTO and ADT libraries, the CITE-seq-count package (v1.4.2) was used (https://github.com/Hoohm/CITE-seq-Count). Count matrices were then used as input into the Seurat R package (v4.0) to perform all downstream analyses
Assembly: hg38, mm10
Library strategy: CaRPool-seq (Cas13 RNA Perturb-seq)

source_name: blood

extract_protocol:
Puromycin selected, perturbed cells were stained with experiment-specific Antibody Derived Tags (ADT) and barcoded with a unique Oligonucleotide Hash Tag (HTO). After Hash- and Cite-tagged cells were counted and checked for viability using a hematocytometer, cells were loaded into a Chromium Controller (10X Genomics).
Gene expression (GEX) libraries were prepared using Chromium Single Cell 3ʹ v3 protocol (10x Genomics). sgRNA (GDO) libraries from direct capture perturb-seq experiments were prepared using the standard feature barcoding  Chromium Single Cell 3ʹ v3 (10x Genomics) workflow. Cellular ADT and HTO libraries were prepared as described on cite-seq.com (CITE-seq_and_Hashing_protocol_190213). CaRPool-seq bcgRNA libraries were prepared as follows:
Library construction for bcgRNA derived oligos largely followed 10x Genomics user guide CG000184 Rev C for Feature Barcoding with some modifications. Specifically, we eluted the GEM-RT in 33ul and added 2µl containing 0.4µM ADT additive primer (for bcgRNAs and ADTs) and 0.2µM HTO additive primer prior to cDNA amplification. The cDNA was purified using 0.6x SPRI cleanup for mRNA fraction. The supernatant containing ADT, HTO, and bcgRNA cDNA was purified was purified by adding another 1.4x SPRI (0.6+1.4 = 2x SPRI) followed by an additional 2x SPRI clean up. The purified short fragments were split evenly into three pools (e.g. 3 x 20µl). One pool each was used for HTO and ADT library construction as described below. Half of the remaining pool (10µl) was used to construct the bcgRNA library using two PCR recipes. PCR1 adds Illumina P5 and P7 handles to the bcgRNA amplicon (100µl PCR1: 50µl 2x KAPA Hifi PCR Mastermix, up to 45µl bcgRNA PCR template, 2.5µl Feature SI Primers 2 10µM, 2.5µl TruSeq Small RNA RPIx primer (containing i7 index) 10µM; 95°C 3min, 12x[95°C 20sec, 60°C 8sec, 72°C 8sec], 72°C 1min). PCR2 amplifies with P5 and P7 primers (100µl PCR2: 50µl 2x KAPA Hifi PCR Mastermix, up to 45µl purified PCR1 product, 2.5µl P5 primer 10µM, 2.5µl P7 primer 10µM; 95°C 3min, 4x[95°C 20sec, 60°C 8sec, 72°C 8sec], 72°C 1min). The final bcgRNA amplicon has a length of 203bp and can be sequenced on a standard Illumina sequencing platform with standard Illumina sequencing primers (>= 28 cycles Read1 and >=15 cycles Read 2).

value: blood

value: Monocyte isolated from peripheral blood from an acute monocytic leukemia patient

tag: library type

value: Cas13d bcgRNA amplicon

tag: antibodies/tags


title: THP1_Cas13d_combinatorial_pooledScreen CD11b_low 400ul_Virus


title: THP1_Cas13d_combinatorial_pooledScreen CD11b_low 300ul_Virus


title: THP1_Cas13d_combinatorial_pooledScreen CD11b_high 400ul_Virus


title: THP1_Cas13d_combinatorial_pooledScreen CD11b_high 600ul_Virus


title: HI47P401218

data_processing:
RTA 3.4.4, bcl2fastq 2.20.0.422 (Illumina)
Before alignment to reference genome each sequence in the raw FASTQ files were trimmed on base call quality and sequencing adapter contamination using Trim Galore! wrapper tool. Reads shorter than 20 bp were removed from FASTQ file. Trimmed reads were aligned to the reference genome using open source short read aligner STAR (https://code.google.com/p/rna-star/) with settings according to log file. Feature counts were determined using R package “Rsubread”. Only genes showing counts greater 5 at least two times across all samples were considered for further analysis (data cleansing). Gene annotation was done by R package “bioMaRt. Before starting the statistical analysis steps,  expression data was log2 transformed and TMM normalized (edgeR).
Assembly: hg38
Supplementary files format and content: Matrix table with TMM-normalizedl log2CPM for every gene and every sample

value: PBMC


title: RT_Tumor_2

tag: strain


title: HI47P401407

value: TNR


title: HI47P601292


title: THP1_Cas13d_combinatorial_pooledScreen CD11b_low 600ul_Virus


title: THP1_Cas13d_combinatorial_pooledScreen Input 600ul_Virus


title: cHiC__limb_E115_wt_mouse_Rep-2

description: mpimg_L5881_L10142_WT-HL-E11.5_S12_S1_merged_enriched_only_MAPQ30.hic

data_processing:
Raw fastq files had read lengths of 75bp and 100bp, respectively. In a preprocessing step, fastq files with 100 bp read length were trimmed to 75bp to achieve comparable initial read lengths for all samples.
Fastq files were processed with the HiCUP pipeline v0.8.1 (no size selection, Nofill: 1, Format: Sanger) for mapping, filtering and deduplication steps (Wingett et al., 2015). The pipeline was set up with Bowtie 2.4.2 for mapping short reads to reference genome mm10 (Langmead and Salzberg, 2012). If replicates were available, they were merged after the processing with the HiCUP pipeline. Binned and KR normalized cHiC maps (Knight and Ruiz, 2012; Rao et al., 2014) were generated using Juicer tools v1.19.02 (Durand et al., 2016). Only read pairs for region chr8:39,030,001-48,000,000 and with MAPQ≥30 were considered for the generation of cHiC maps.
Additional to the original cHiC maps, custom reference genomes were derived from mm10  for the three deletions (ΔD1, ΔD2, ΔD1+2), considering the respective deletions and cHiC data was processed correspondingly. cHiC maps were displayed as heatmaps in which very high values were truncated to improve the visualization.
Genome_build: mm10 and custom mutant genomes
Supplementary_files_format_and_content: .hic .mutants are mapped on both wt and corresponding mutant mm10 genomes (see description for each sample)

growth_protocol: Mouse G4 ESCs (XY, 129S6/SvEvTac x C57BL/6Ncr F1 hybrid) were grown as described previously on a mitomycin-inactivated CD1 mouse embryonic fibroblast feeder monolayer on gelatinised dishes  at 37oC, 7.5% CO2 (Andrey and Spielmann, 2017; George et al., 2007). ESCs were cultured in ESC medium containing knockout DMEM with 4,5 mg/ml glucose and sodium pyruvate supplemented with 15% FCS, 10 mM Glutamine, 1x penicillin/streptomycin, 1x non-essential amino acids, 1x nucleosides, 0.1 mM beta-Mercaptoethanol and 1000 U/ml LIF. Medium was changed every day while G4-cells were split every 2-3 days or were frozen at 1x 106 cells/cryovial in ESC medium containing 20% FCS and 10% DMSO. ESCs and feeder cells were tested for Mycoplasma contamination using the MycoAlert detection kit and MycoAlert Assay Control Set.    E11.5 forelimb cells were isolated from C57BL/6 embryonic limbs through trypsinization, filtration (100 µm) and centrifugation.

extract_protocol:
3C libraries were prepared from fixed nuclei as described previously (Kragesteen et al, 2018). Briefly, lysis buffer was removed by centrifugation at 400 g for 5 min at 4 °C, followed by supernatant aspiration, snap-freezing, and pellet storage at − 80 °C. Later, nuclei pellets were thawed on ice, resuspended in 520 μl 1× DpnII buffer, and then incubated with 7.4 μl 20% SDS shaking at 900 rpm. at 37 °C for 1 h. Next, 75 μl 20% Triton X-100 was added and the pellet was left shaking at 900 rpm at 37°C for 1 h. A 15-μl aliquot was taken as a control for undigested chromatin (stored at − 20°C). The chromatin was digested using 40 μl 10 U/μl DpnII buffer shaking at 900 rpm at 37°C for 6 h; 40 μl of DpnII was added and samples were incubated overnight, shaking at 900 rpm. at 37°C. On day three, 20 μl DpnII buffer was added to the samples followed by shaking for an additional 5 h at 900 rpm. at 37 °C. DpnII subsequently was inactivated at 65 °C for 25 min and a 50-μl aliquot was taken to test digestion efficiency (stored at − 20 °C). Next, digested chromatin was diluted in 5.1 ml H2O, 700 μl 10× ligation buffer, 5 μl 30 U/μl T4 DNA ligase and incubated at 16°C for 4 h while rotating. Ligated samples were incubated for a further 30 min at room temperature. Chimeric chromatin products and test aliquots were de-cross-linked overnight by adding 30 μl and 5 μl proteinase K, respectively, and incubated at 65 °C overnight. On the fourth day, 30 μl or 5 μl of 10 mg ml−1 RNase was added to the samples and aliquots, respectively, and incubated for 45 min at 37°C. Next, chromatin was precipitated by adding 1 volume phenol-chloroform to the samples and aliquots, vigorously shaking them, followed by centrifugation at 4,000 rpm at room temperature for 15 min. To precipitate aliquot chromatin, 1 volume 100% ethanol and 0.1 volume 3M NaAc, pH 5.6 was added and the aliquots placed at -80°C for 30 min. DNA was then precipitated by centrifugation at 5,000 rpm. for 45 min at 4°C followed by washing with 70% ethanol, and resuspension in 20 μl with 10 mM Tris-HCl, pH 7.5. To precipitate samples, extracted sample aqueous phases were mixed with 7 ml H2O, 1 ml 3M NaAc, pH 5.6, and 35 ml 100% ethanol. Following incubation at −20°C for at least 3 h, precipitated chromatin was isolated by centrifugation at 5,000 rpm for 45 min at 4 °C. The chromatin pellet was washed with 70% ethanol and further centrifuged at 5,000 rpm for 15 min at 4 °C. Finally, 3C library chromatin pellets were dried at room temperature and resuspended in 10 mM Tris-HCl, pH 7.5. To check the 3C library, 600 ng were loaded on a 1% gel together with the undigested and digested aliquots.
The 3C library was then sheared using a Covaris sonicator (duty cycle: 10%; intensity: 5; cycles per burst: 200; time: 6 cycles of 60 s each; set mode: frequency sweeping; temperature: 4–7 °C). Adaptors were added to the sheared DNA and amplified according to the manufacturer’s instructions for Illumina sequencing (Agilent). The library was hybridised to the custom designed SureSelect beads and indexed for sequencing (75–100 bp paired-end) following the manufacturer’s instructions (Agilent).

treatment_protocol: Disassociated ESCs and limb cells were transferred to a 50-ml falcon tube and complemented with 10% FCS/PBS. 37% formaldehyde was added to a final concentration of 2% and cells were fixed for 10 min at room temperature. Crosslinking was quenched by adding glycine (final concentration; 125 mM). Fixed cells were washed twice with cold PBS and lysed using fresh lysis buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA with protease inhibitor) to isolate nuclei. Cell lysis was assessed microscopically after 10-min incubation in ice. Nuclei were centrifuged for 5 min at 480g, washed once with PBS and snap frozen in liquid N2.

tag: group

tag: genotype

value: wt


title: cHiC__ESC_G4_wt_mouse_Rep-1

description: mpimg_L13065_L13736_ESC-G4-cHiC-_S2_S6_merged_enriched_only_MAPQ30.hic


title: cHiC__limb_E115_wt_mouse_Rep-1


title: HI47P200749

extract_protocol:
The “PAXgene Blood miRNA Kit” (Qiagen) was used for the purification of miRNA  and total RNA.
100ng total RNA was depleted for rRNA and globin by using QIAseq® FastSelectTM RNA Removal Kit (Qiagen). The RNA Sequencing library was prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs). The libraries were sequenced on Illumina NovaSeq6000 using NovaSeq6000 S2 Reagent Kit (100 cycles, paired ended run) with an average of 50 Mio reads per RNA sample.

tag: phenotype


title: THP1_Cas13d_combinatorial_pooledScreen Input 400ul_Virus


title: THP1_Cas13d_combinatorial_pooledScreen Input 300ul_Virus


title: HEK293FT cells, GDO-derived cDNA

description:
guide RNA library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Tag reads
Guide-derived oligonucleotide (GDO)
Perturb-seq.GEXGDO.barcodes.tsv.gz
Perturb-seq.GEXGDO.features.tsv.gz
Perturb-seq.GEXGDO.matrix.mtx.gz
Perturb-seq.metadata.tsv.gz
Perturb-seq.GDO.feature_ref.csv.gz

source_name: kidney

value: kidney

value: epithelial embryonic kidney cells

value: GDO


title: HI47P500256

tag: donor


title: HI47P100757


title: HI47P000756


title: HI47P000242


title: HI47P101396


title: HEK293FT cells, ADT-derived cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
Perturb-seq.ADT.barcodes.tsv.gz
Perturb-seq.ADT.features.tsv.gz
Perturb-seq.ADT.matrix.mtx.gz
Perturb-seq.metadata.tsv.gz
Perturb-seq.ADT.feature_ref.csv.gz

value: ADT

value: CD46 TotalSeq™-A0858,  CD55 TotalSeq™-A0383,  CD71 TotalSeq™-A0394,  CD29 TotalSeq™-A0369,  CD56 TotalSeq™-A0047, CD59 TotalSeq™-A0361


title: HEK293FT cells, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
Perturb-seq.HTO.barcodes.tsv.gz
Perturb-seq.HTO.features.tsv.gz
Perturb-seq.HTO.matrix.mtx.gz
Perturb-seq.metadata.tsv.gz
Perturb-seq.HTO.feature_ref.csv.gz

value: HTO

value: anti-B2M (Purified anti-human β2-microglobulin [2M2]), anti-CD298 clone:LNH-94


title: HEK293FT cells, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
Perturb-seq.GEXGDO.barcodes.tsv.gz
Perturb-seq.GEXGDO.features.tsv.gz
Perturb-seq.GEXGDO.matrix.mtx.gz
Perturb-seq.metadata.tsv.gz

value: mRNA


title: HI47P900232


title: HI47P400714


title: HI47P701293


title: HI47P301415


title: HI47P102782


title: HI47P301352


title: HI47P500751


title: HI47P200776


title: latent iSLK.219 + iSLK.H

city: Madison

first: Marta

middle: Maria

last: Gaglia

state: WI

address: 1525 Linden Dr

institute: University of Wisconsin Madison

data_processing:
Raw sequencing data (.bcl files) were processed using the 10X Genomics CellRanger (3.0.0) software
Fastq files were generated for the reads using the mkfastq function as described on the 10X Genomics website
The CellRanger count function was used to align the reads to a reference genome
The matrix table of gene counts from CellRanger was used as an input for integration and clustering analyses using the R-based Seurat package (version 3.1.1.9021, R version 3.6.1)
Genome_build: human: GRCh38; KSHV: GQ994935.1; RFP/GFP/PAC cassette insertion in rKSHV.219: MZ617352
Supplementary_files_format_and_content: Each 10x genomics library consists of 3 date files (matrix, features, barcodes). The matrix file is a sparse matrix that represents the measured read counts for a given pair of index values for the feature and barcode (each barcode represents an individual cell). The feature and barcode files represent the names of the features and the barcodes for each index.

source_name: iSLK.219 and iSLK.H cells

growth_protocol: iSLK.H and iSLH.219 cell lines were grown in DMEM+10% FBS.

extract_protocol:
Single cell samples were generated according to 10x Genomics' sample preparation protocol for cultured cell lines (CG00054) and Gel Beads-in-emulsion (GEM) generation protocol (CG000183). Briefly, cells were trypsinized and washed twice with dPBS. Cells were resuspended in dPBS and passed through a 30 µm strainer to remove clumps. Cells were counted and diluted to a concentration of 1,000,000 cells/mL. Cells were mixed with a reverse transcription mastermix (including a primer with polydT anchor) and loaded onto a Chromium B microfluidic chip. Gel beads and partitioning oil were loaded onto the chip and the chip was run through the chromium controller device to generate the GEMs. GEMs were incubated in a thermal cycler for 1 cycle to generate cDNA. The emulsion was broken and cDNA was isolated with magnetic beads, amplified for 12 cycles, and then cleaned up with SPRIselect reagent.
Libraries were prepared according to 10x Genomics' library construction procol (CG000183). Briefly, cDNA was fragmented and then end-repaired and a-tailed with the enzymes in the provided 10x genomics kit (version 3, PN-1000092). cDNA was double sided size selected using SPRIselect and adaptor oligos were ligated onto the cDNA and further cleaned up with SPRIselect.

treatment_protocol: Samples were collected after 4 days of treatment.

tag: kshv strain

tag: lytic induction

tag: caspase inhibitor treatment

value: vehicle (DMSO)

tag: anti-ifn treatment

value: vehicle (PBS)


title: lytic iSLK.219 + casp-i + anti-IFN

source_name: iSLK.219 cells

value: 1 ug/ml doxycycline for 4 days

value: 1:500 dilution anti-IFN antibody cocktail - cat # 39000-1;PBL Assay Science


title: lytic iSLK.219


title: HI47P200262

tag: tissue

value: Lymphoycyte


title: HI47P801500

tag: cell type


title: HI47P701266

tag: time


title: HI47P200730


title: cHiC__ESC_G4_wt_mouse_Rep-2


title: lytic iSLK.219 + casp-i


title: HI47P100261


title: HI47P001304


title: HI47P100702


title: HI47P601472


title: HI47P500201


title: HI47P000224


title: HI47P600266


title: HI47P700726


title: HI47P600743


title: HI47P101350


title: MDA-MB-468 cells, LSW 2

data_processing:
Quality control of RNA-seq raw paired data was performed using FastQC  and MultiQC.
Trim Galore was used to trim adapters, reads with low quality (<30) and short length (<50 bp).
RNA-seq reads were mapped to Homo_sapiens.GRCh38.100 using Hisat2 with default codes.
Sam files were transformed into bam files using samtools.
The read counts of each genes were summarized using featureCounts.
Assembly: Homo_sapiens.GRCh38.100
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco® by Life Technology) with 10% FBS and 1% (v/v) penicillin/streptomycin, and were kept at 37 °C and 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen) according to manufacturer’s instructions and quantified using a Nanodrop Spectophotometer 2000c (Thermo Fisher Scientific). A total amount of 3 μg RNA per sample was used as input material for library construction.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, Ipswich, Massachusetts, USA) following manufacturer’s instruction. Libraries were pooled in equimolar and sequenced using the paired-end strategy (2 × 150) on the Illumina NovaSeq 6000 platform following the standard protocols (Novogene, UK).

treatment_protocol: MDA-MB-468 cells were treated with Limonium Sinense Water extract (LSW) for 48 hours at 500 μg/mL

tag: cell line

value: breast cancer cells

value: WT

tag: treatment

value: LSW, 500 microg/mL, 48 hours


title: MDA-MB-468 cells, Control 3