title: Astrocytes, mock, rep1

city: Hannover

first: Ulrich

last: Kalinke

state: Lower Saxony

address: Feodor-Lynen-Str. 7

department: Institute for Experimental Infection Research

institute: Twincore, Centre for Experimental and Clinical Infection Research

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control of the sequenced raw FASTQ-files was performed with FastQC software (version 0.11.9) and mapped to Ensembl mouse genome reference version GRCm38 (mm10) using STAR (version 2.5.4b). Gene abundance was also determined by Feature Counts (version 1.6.0) software using respective Ensembl GTF annotations.
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw counts for every gene and there corresponding Ensembl ID

source_name: Brain

extract_protocol:
The immunoprecipitated RNA was purified using the RNeasy Mini Kit (Qiagen) according to manufacturer's instructions. RNA quality and concentrations were accessed using Bioanalyzer RNA kit and samples with RIN values > 8.0 were selected for library preparation.
RNA libraries for RNA-seq were prepared using NEBNext Low input RNA library Prep Kit for Illumina (NEB, E6420) following manufacturer's protocols.

value: Brain

value: Astrocytes

value: GFAP-Cre+/- Rpl22HA/wt

value: mock

tag: timepoint

value: 3 weeks

tag: batch

tag: biological replicate

value: Rep 1


title: gq_sample_151

status: Public on Jul 11 2023

type: SRA

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

library_source: transcriptomic

data_processing:
All sequencing data was extracted from FASTQ files and processed using CASAVA 1.8+
Illumina adapter sequences were trimmed using the Fastx_toolkit
Bowtie was used to align reads to the human genome
Rfam database was used to map reads to known snoRNAs
Sequencing data was normmalized with the Bioconductor-DESeq2 package
Assembly: GRch37

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
Total RNA was isolated from whole blood using PAXgene Blood RNA kit (Qiagen) according to manufacturer's instructions
Libraries prepared using Illumina TruSeq Small RNA protocol following manufactuer's instructions.

tag: tissue

value: Peripheral blood

tag: treatment

value: Placebo

tag: sample type

value: Week 8 Responder


title: NT-2-Dexa-rep3

city: Amsterdam

first: Isabel

last: Mayayo-Peralta

address: Plesmanlaan 121

country: Netherlands

institute: NKI

data_processing:
Sequencing data were aligned to the human reference genome hg38 using HISAT2 (v2.1.0), and the number of reads per gene was measured with HTSeq count (v0.5.3)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count values for each Sample

growth_protocol: DMEM/F12 (1:1) (1x) + Glutamax + 10% FCS + 1% Pen/Strep, cultured at 5% CO2 and 37 °C.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen, Germany) following manufacturer´s instructions.

treatment_protocol: Cells were treated with DMSO(vhcl) or 100nM Dexamethasone for 8 hours

tag: cell line

tag: genotype

value: DEXA

tag: time

value: 8 hours


title: STAG2KO-Dexa-rep3


title: NT-2-Dexa-rep2


title: Astrocytes, cuprizone, rep1

country: Germany

molecule: polyA RNA

organism: Mus musculus

tag: cell type

value: cuprizone


title: STAG2KO-Dexa-rep2


title: Scr-static_1

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content, and duplication rates with FastQC.
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides
Trimmed and filtered reads were aligned vs. the Ensembl human genome version hg38 (GRCh38) using STAR 2.5.2b with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.14.1. Only genes with a minimum fold change of ±1.5 (log2 ± 0.59), a maximum Benjamini–Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
Assembly: hg38
Supplementary files format and content: lirary-size normalized count matrix

source_name: Human Umbilical Vein Endothelial Cells

growth_protocol: HUVECs were obtained from Lonza and were cultured in endothelial growth medium (EGM-2; Lonza) according to the manufacturer’s instructions.

extract_protocol:
Total RNA was isolated from endothelial cell monolayers using the Quick-RNA Micro prep kit according to the manufacturer’s protocol.
Total RNA libraries were obtained by rRNA depletion with RiboMinus Eukaryote System v2 (Thermo Fisher) followed by Ion Total RNA-Seq Kit v2 (Thermo Fisher) according to manufacturer protocol.

treatment_protocol: HUVECs were seeded in µ-slide I0.4 Luer ibiTreat chambers and were transfected with control siRNA at 70% confluence. After transfection, HUVECs were exposed to 48 h laminar flow versus cells kept for 48 h under static conditions. Laminar flow was applied by using the ibidi pump system.

value: Human Umbilical Vein Endothelial Cells


title: Scr-static_2


title: Scr-flow_2


title: gq_sample_150


title: Scr-flow_1


title: Dietchange_RD_FD_RD_Ileum_3

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

description: Ileum, 12 days after first switch, sample #3

data_processing:
Sequencing quality was assessed with FastQC v. 0.11.5, followed by trimming of low quality bases with Trimmomatic v. 0.33 and alignment to the Mus musculus genome draft GRCm38.84 using STAR v. 2.5.0.
Assembly: GRCm38.84
Supplementary files format and content: Raw counts summarized per gene for each sample after alignment with STAR

source_name: Ileum

extract_protocol:
Peyer’s patches (PPs) were removed from small intestine (SI) and put in TriFastTM (PeqLab, Cat.Nr.: 30-2010). Small intestine was divided into duodenum, jejunum and ileum and each segment was put in TriFastTM. Total RNA was purified using the NucleoSpin RNA II kit (Macherey & Nagel), according to manufacturer’s instructions. RNA sequencing was performed on total PPs, ileum or FACS-sorted CD4+Foxp3- or CD45.1+ OT-II viable T cells isolated from PPs or dLN, respectively
For library preparation of total PPs and ileum samples, cDNA was used as input to construct 250~300 bp insert cDNA libraries using NEBNext® UltraTM RNA Library Prep Kit (New England Biolabs, Ipswich, USA). Indices were included to multiplex multiple samples. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. For FACS-sorted cells, total RNA was amplified using SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing (Takara Bio USA, Inc., Mountain View, USA) with the double strand cDNA (ds-cDNA) being synthesized. Then ds-cDNA was purified with AMPure XP beads and quantified with Qubit (Life TechnologiesTM).  The library was ready after end repair, A-tailing, adapter ligation, and size selection. After amplification and purification, insert size of the library was validated on an Agilent 2100 and quantified using quantitative PCR (Q-PCR).

value: Ileum

value: diet change 3 days RD, 3 days FD, 3 days RD

value: regular diet


title: NT-2-Dexa-rep1


title: Dietchange_RD_FD_RD_Ileum_2

description: Ileum, 12 days after first switch, sample #2


title: Astrocytes, mock, rep2

value: Rep 2


title: STAG2KO-Dexa-rep1


title: gq_sample_149

value: Week 8 Non-Responder


title: Dietchange_RD_FD_RD_Ileum_1

description: Ileum, 12 days after first switch, sample #1


title: NT-2-DMSO-rep3

value: DMSO


title: gq_sample_148

value: Duloxetine


title: Dietchange_RD_FD_Ileum_3

description: Ileum, 9 days after first switch, sample #3

value: diet change 3 days RD, 3 days FD

value: feast diet


title: gq_sample_147


title: STAG2KO-DMSO-rep3


title: Astrocytes, cuprizone, rep2

value: Brain

value: Astrocytes

value: GFAP-Cre+/- Rpl22HA/wt

value: 3 weeks


title: Colon_HSDiet_malemouse_4,5

type: RNA

city: Hamilton

first: Zarwa

last: Saqib

state: ON

address: 1280 Main St W

institute: McMaster University

hyb_protocol: The protocol followed was according to manufacturer's intructions

data_processing: After extraction and data collection by the nanostring digital analyzer, the RCC files generated were imported into the nSolver4.0 software (desktop version). The RCC files comprising the counts of each sample were inspected and checked for quality scores of each sample followed by a postive control normalization and a reference (housekeeping) gene normalization for each sample.

label: color-coded barcode technology

source_name: Colon tissue from male mice # 4, 5 on High Salt Diet

extract_protocol: RNeasy Mini Kit from Qiagen (Toronto, Canada) was used to extract total RNA from mouse colonic tissues, according to the manufacturer's instructions. RNase-free DNase from Qiagen was also used to carry out DNase digestion during RNA purification.

value: Colonic sections tissue

tag: gender

value: male

tag: diet

value: high salt diet


title: Colon_HSDiet_femalemouse_1,2,3

source_name: Colon tissue from female mice # 1, 2, 3 on High Salt Diet

label_protocol: The protocol followed was according to manufacturer's intructions

value: female


title: Dietchange_RD_FD_Ileum_2

description: Ileum, 9 days after first switch, sample #2

value: Ileum


title: NT-2-DMSO-rep2

value: 8 hours


title: gq_sample_146

value: Peripheral blood

value: Week 8 Responder


title: gq_sample_145


title: STAG2KO-DMSO-rep2


title: gq_sample_144

value: Placebo


title: gq_sample_15

value: Week 0 Non-Responder


title: Dietchange_RD_FD_Ileum_1

description: Ileum, 9 days after first switch, sample #1


title: Colon_ControlDiet_femalemouse_4,5

source_name: Colon tissue from female mice # 4, 5 on Control Diet

value: control diet


title: Baseline_RD_9days_Ileum_2

description: Ileum, 6 days after first switch, sample #2

value: baseline 9 days of regular diet

value: regular diet


title: Colon_HSDiet_malemouse_1,2,3

source_name: Colon tissue from male mice # 1, 2, 3 on High Salt Diet


title: NT-2-DMSO-rep1

value: DMSO


title: STAG2KO-DMSO-rep1


title: Baseline_RD_9days_Ileum_3

description: Ileum, 6 days after first switch, sample #3


title: Colon_ControlDiet_femalemouse_1,2,3

source_name: Colon tissue from female mice # 1, 2, 3 on Control Diet


title: Colon_HSDiet_femalemouse_4,5

source_name: Colon tissue from female mice # 4, 5 on High Salt Diet


title: Colon_ControlDiet_malemouse_4,5

source_name: Colon tissue from male mice # 4, 5 on Control Diet


title: Baseline_RD_9days_Ileum_1

description: Ileum, 6 days after first switch, sample #1


title: gq_sample_143


title: Baseline_RD_6days_Ileum_3

description: Ileum, 3 days after first switch, sample #3

value: baseline 6 days of regular diet


title: PAXIP1-KO/NT mixed input [H3K4me1_9]

library_source: genomic

data_processing:
All reads were aligned to the Human Reference Genome (GRCh38.102) using Burrows-Wheeler Aligner (v0.7.17 )
Reads were filtered based on MAPQ quality ≥20 (samtools v1.9), and duplicate reads were removed
Peak calling over input was generated by using MACS2 (v2.1.2)
Assembly: GRCh38.102
Supplementary files format and content: narrowPeak

molecule: genomic DNA

extract_protocol:
Chromatin immunoprecipitation followed by sequencing (ChIP)-seq was performed as previously described (Schmidt, D. et al. Methods 48, 240–248 (2009).In brief, cells were fixed in 1% formaldehyde for 10 min and quenched with 0.125M glycine. Nuclear lysates were extracted as previously described and sonicated for 13 cycles (30 sec on/30 sec off) using the Bioruptor® Pico (B01060001, Diagenode). ). Per ChIP, 50 µL of magnetic Protein A beads (10008D, Thermo Fisher Sci-entific) beads were conjugated to 7.5µL of GR antibody, or 5µg of RAD21, PAXIP1, and H3K4me1 antibodies.
Immunoprecipitated DNA was processed for library preparation usin KAPA library preparation kit, KK8234, Roche.

treatment_protocol: Cells were treated with vDMSO(vhcl) or 100nM Dexamethasone for 2 hours

value: Lung Cancer

value: mixed

tag: treatment length

tag: chip antibody


title: gq_sample_142

value: Week 0 Responder


title: YUMM-3w-IFNg-24-n3

city: Cambridge

first: Mario

last: Niepel

state: MA

address: 35 Cambridgepark Dr Suite 300

country: USA

institute: Ribon Therapeutics, Inc.

data_processing:
Raw transcriptome sequences were analyzed using Salmon v0.13.1.
Using Salmon’s mapping-based mode with a Gencode (release 20) mouse reference transcriptome index produced transcriptome read counts for each sequenced sample.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Skin

growth_protocol: YUMM2.1 and CT26 cells were cultured with or without 50 IU/mL of IFN-γ in complete medium of RPMI-1640 supplemented with 10% FBS and 1% Penicillin/Streptomycin for a period of up to 3 weeks.

extract_protocol:
RNA was isolated from triplicate experiments using the Qiagen RNeasy mini kit (catalog # 74106) per manufacturer’s instructions.  RNA concentration was determined using a NanoDrop 8000 (ThermoFisher Scientific, Waltham, MA).
High-throughput 3’ digital gene expression were measured based on a previously published protocol (Massachusetts Institute of Technology, Cambridge, MA) (Soumillon, 2014).

treatment_protocol: Prior to the final 48-hour harvesting, cells were plated at a density of 2 × 105 cells/well in a 6-well dish and allowed to grow until the time of harvesting.

value: Skin

value: Melanoma

value: IFNG (50 IU/mL)

value: 3 week and 24 hour


title: Colon_ControlDiet_malemouse_1,2,3

source_name: Colon tissue from male mice # 1, 2, 3 on Control Diet

value: Colonic sections tissue

value: male


title: gq_sample_141

value: Peripheral blood


title: Baseline_RD_6days_Ileum_2

description: Ileum, 3 days after first switch, sample #2

value: Ileum


title: YUMM-3w-IFNg-24-n2


title: A549-PAXIP1KO-rep1+Dex(100nM) [H3K4me1_7]

value: 100nM Dexamethasone

value: H3K4me1 (ab8895, abcam)


title: A549-PAXIP1KO-rep2+Dex(100nM) [H3K4me1_8]


title: Baseline_RD_6days_Ileum_1

description: Ileum, 3 days after first switch, sample #1


title: YUMM-3w-IFNg-24-n1


title: A549-PAXIP1KO-rep2-vhcl [H3K4me1_6]


title: gq_sample_14

value: Placebo


title: A549-PAXIP1KO-rep1-vhcl [H3K4me1_5]


title: YUMM-3w-IFNg-2-n3

value: 3 week and 2 hour


title: gq_sample_139

value: Week 0 Non-Responder


title: Baseline_RD_3days_Ileum_3

description: Ileum, 0 days after first switch, sample #3

value: baseline 3 days of regular diet

value: regular diet


title: gq_sample_138


title: A549-NT(1)-rep2+Dex(100nM) [H3K4me1_4]

value: Lung Cancer


title: YUMM-3w-IFNg-2-n2


title: Baseline_RD_3days_Ileum_1

description: Ileum, 0 days after first switch, sample #1


title: YUMM-3w-IFNg-2-n1


title: gq_sample_137

value: Duloxetine

value: Week 0 Responder


title: A549-NT(1)-rep1+Dex(100nM) [H3K4me1_3]


title: YUMM-3w-IFNg-0-n3

value: Skin

value: Melanoma

value: 3 week and 0 hour


title: SOCS3KO_Tcells_scATACseq

city: Shinjuku-ku

first: Setsuko

last: Mise-Omata

state: Tokyo

address: 35 Shinanomachi

department: Department of Microbiology and Immunology

country: Japan

institute: Keio University

library_source: genomic single cell

data_processing:
WT and KO sample were applied cellranger-atac mkfastq for demultiplexing the raw base call (BCL) files and continuing with cellranger-atac count for single library analysis, separately (CellRanger ATAC v2.1).  The samples were aggregated with a single instance of cellranger-atac aggr.
Assembly: mm10
Supplementary files format and content: .mtx counts matrix; .tsv cell barcodes list; .fragments.tsv.gz fragments file; .fragments.tsv.gz.tbi fragments index file
Supplementary files format and content: .csv Tab-separated values files

source_name: MC38 tumor

extract_protocol:
MC38 tumor mass were excised and minced and digested with 0.25% Liberase TM (Merck) and 20 kU/mL DNase I (Sigma-Aldrich, St Louis, MO) at 37 °C for 30 minutes with gentle shaking. Cells were passed through a 100-μm filter and subjected to 40% Percoll centrifugation to remove debris and epithelial cells from the surface of the solution. Red blood cell lysis was performed if necessary, and the cells were washed twice with phosphate-buffered saline (PBS). The cells were incubated with anti-CD3e+-Brilliant violet-421 , anti-TCRb+-APC antibodies, and Fixable viabily dye -eFlour 780. CD3e+ TCRb+ cells were isolated by FACS AriaIII.
Library was performed according to the manufacter’s instructions (Chromium Next GEM SIngle Cell ATAC Reagent Kits v2, 10x Genomics). The isolated nuclei suspension was diluted and then incubated with transposition mix for a targeted nuclei recovery of 10,000 cells. GEMs were then captured on the chromium NEXT GEM Chip H (10X Genomics 2000180). Following GEM incubation, clean up was performed using Dynabeads MyOne Silane beads (10X Genomics 2000048) and SPRIselect reagent (Beckman Coulter B23318). Finally, the library was amplified for a total of 7 Sample Index PCR cycles (WT, A3; KO, A4).

treatment_protocol: MC38 (2 x 10^6 cells/mouse) were subcutaneously inoculated into the right flank of two WT Socs3f/f and two Cd4Cre Socs3f/f mice. On day 12, the CD3e and TCRb+ cells of tumor tissue from each implanted mouse were used as a single-cell ATAC sequencing sample.

value: MC38 tumor

value: T cells

value: TIL

value: no treatment


title: gq_sample_136

value: Peripheral blood

value: Week 8 Non-Responder


title: A549-NT(1)-rep2-vhcl [H3K4me1_2]

value: DMSO

value: H3K4me1 (ab8895, abcam)


title: gq_sample_135

value: Placebo


title: A549-NT(1)-rep1-vhcl [H3K4me1_1]


title: YUMM-3w-IFNg-0-n1

value: IFNG (50 IU/mL)


title: gq_sample_140


title: PAXIP1-KO/NT mixed input [PAXIP1_9]

value: mixed


title: 7 weeks Astrocytes, cuprizone, rep3

description: Astrocytes, cuprizone, rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control of the sequenced raw FASTQ-files was performed with FastQC software (version 0.11.9) and mapped to Ensembl mouse genome reference version GRCm38 (mm10) for batch1 and GRCm39 (mm39) for batch2 using STAR (version 2.5.4b). Gene abundance was also determined by Feature Counts (version 1.6.0) software using respective Ensembl GTF annotations.
Assembly: GRCm38/GRCm39
Supplementary files format and content: Matrix table with raw counts for every gene and there corresponding Ensembl ID

value: Brain

value: Astrocytes

value: GFAP-Cre+/- Rpl22HA/wt

value: cuprizone

value: 7 weeks

tag: biological replicates

value: Rep 3


title: gq_sample_134

value: Duloxetine

value: Week 0 Responder


title: 7 weeks Astrocytes, cuprizone, rep2

description: Astrocytes, cuprizone, rep2

value: Rep 2


title: A549-PAXIP1KO-rep2+Dex(100nM) [PAXIP1_8]

value: Lung Cancer

value: 100nM Dexamethasone

value: PAXIP1(ab70434, abcam)


title: YUMM-3w-Ctrl-0-n3

value: Skin

value: Melanoma

value: BSA (0 IU/mL)

value: 3 week and 0 hour


title: Baseline_RD_3days_Ileum_2

description: Ileum, 0 days after first switch, sample #2

value: Ileum

value: baseline 3 days of regular diet

value: regular diet


title: 7 weeks Astrocytes, cuprizone, rep1

description: Astrocytes, cuprizone, rep1

value: Brain

value: Astrocytes

value: GFAP-Cre+/- Rpl22HA/wt

value: Rep 1


title: YUMM-3w-Ctrl-0-n2


title: YUMM-3w-Ctrl-0-n1


title: A549-PAXIP1KO-rep2-vhcl [PAXIP1_6]

value: DMSO


title: 7 weeks Astrocytes, mock, rep3

description: Astrocytes, mock, rep3

value: mock

value: 7 weeks

value: Rep 3


title: A549-PAXIP1KO-rep1+Dex(100nM) [PAXIP1_7]

value: Lung Cancer

value: 100nM Dexamethasone


title: gq_sample_132

value: Peripheral blood

value: Duloxetine

value: Week 0 Non-Responder


title: gq_sample_133

value: Week 0 Responder


title: 7 weeks Astrocytes, mock, rep2

description: Astrocytes, mock, rep2

value: Rep 2


title: YUMM-3w-IFNg-0-n2

value: Skin

value: Melanoma

value: IFNG (50 IU/mL)

value: 3 week and 0 hour


title: A549-PAXIP1KO-rep1-vhcl [PAXIP1_5]

value: PAXIP1(ab70434, abcam)


title: gq_sample_130


title: YUMM-2w-IFNg-24-n3

value: 2 week and 24 hour


title: 7 weeks Astrocytes, mock, rep1

description: Astrocytes, mock, rep1

value: Brain

value: Astrocytes

value: GFAP-Cre+/- Rpl22HA/wt

value: Rep 1


title: YUMM-2w-IFNg-24-n2


title: gq_sample_13


title: SOCS3WT_Tcells_scATACseq

description: 10x Genomics

value: MC38 tumor

value: T cells

value: TIL

value: WT

value: no treatment


title: gq_sample_131

value: Peripheral blood

value: Duloxetine

value: Week 0 Responder


title: YUMM-2w-IFNg-24-n1

value: Skin

value: Melanoma


title: A549-NT(1)-rep1+Dex(100nM) [PAXIP1_3]

value: Lung Cancer

value: 100nM Dexamethasone


title: A549-NT(1)-rep2+Dex(100nM) [PAXIP1_4]

value: PAXIP1(ab70434, abcam)


title: gq_sample_129

value: Placebo


title: 5.5 weeks Astrocytes, cuprizone, rep2

description: Astrocytes, cuprizone, rep2

value: Brain

value: Astrocytes

value: cuprizone

value: 5.5 weeks

value: Rep 2


title: YUMM-2w-IFNg-2-n3

value: IFNG (50 IU/mL)

value: 2 week and 2 hour


title: A549-NT(1)-rep2-vhcl [PAXIP1_2]

value: DMSO


title: gq_sample_128

value: Peripheral blood


title: 5.5 weeks Astrocytes, cuprizone, rep1

description: Astrocytes, cuprizone, rep1

value: GFAP-Cre+/- Rpl22HA/wt

value: Rep 1


title: YUMM-2w-IFNg-2-n2

value: Skin


title: A549-NT(1)-rep1-vhcl [PAXIP1_1]


title: gq_sample_127

value: Duloxetine

value: Week 0 Responder


title: YUMM-2w-IFNg-2-n1

value: Melanoma


title: gq_sample_126

value: Week 0 Non-Responder


title: 5.5 weeks Astrocytes, mock, rep2

description: Astrocytes, mock, rep2

value: mock


title: 5.5 weeks Astrocytes, mock, rep3

description: Astrocytes, mock, rep3

value: Brain

value: Rep 3


title: YUMM-2w-IFNg-0-n3

value: 2 week and 0 hour


title: HAP, PBRM1KO, IFNg, Rep2

city: Boston

first: Bin

middle: E

last: Li

state: Massachusetts

address: 1 Blackfan Circle Karp Research Building Boston Children's Hospital Boston MA 02115

department: Hematology/Oncology

institute: Boston Children's Hospital

data_processing:
Sequence reads were QC-ed using fastqc version 0.11.3 and trimmed for adaptor sequence/low-quality sequence.
Trimmed sequence reads were mapped to hg19 using STAR aligner version 2.5.2b with default parameters. Gene counts were generated using featureCounts version 2.0.1 with default parameters. Gene counts were then extracted and merged to obtain final raw counts for each gene.
Normalization and the discovery of differentially expressed genes were performed using DESeq2 version 1.34.0 in R 4.1.2 with default parameters.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw count values for each sample

growth_protocol: HAP1 cells were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
HAP1-Cas9 cells were first established by lentiviral introduction of Cas9 and Pbrm1 were knockouted in bulk using sgRNA. Infected cells were selected with both blasticidin and puromycin to ensure cells expression both Cas9 and sgRNA. Pbrm1-intact and Pbrm1-deficient cells were treated with or without 50 ng/mL. IFNg for 5 days. RNA was harvested using RNeasy Mini Plus kit (Qiagen) and resultant RNA were Dnase-treated before library preparation. 200 ng RNA were used for subsequent library preparation
RNA-seq libraries were prepared from poly-A-enriched mRNA using a KAPA mRNA HyperPrep Kit (Roche) and sequenced on an Illumina Novaseq.

treatment_protocol: Pbrm1-intact and Pbrm1-deficient HAP1 cells were treated with or without 50 ng/mL IFNg for 5 days, respectively.

value: myeloid leukemia cells

value: IFNg treated


title: gq_sample_124

value: Week 8 Responder


title: gq_sample_125


title: 5 weeks Astrocytes, mock, rep2

description: Astrocytes, mock, rep2

value: Astrocytes

value: 5 weeks

value: Rep 2


title: YUMM-2w-IFNg-0-n1

value: IFNG (50 IU/mL)


title: HAP, PBRM1KO, IFNg, Rep3


title: 5.5 weeks Astrocytes, cuprizone, rep3

description: Astrocytes, cuprizone, rep3

value: GFAP-Cre+/- Rpl22HA/wt

value: cuprizone

value: 5.5 weeks


title: 5.5 weeks Astrocytes, mock, rep1

description: Astrocytes, mock, rep1

value: Rep 1


title: YUMM-2w-IFNg-0-n2

value: Skin

value: Melanoma


title: 5 weeks Astrocytes, mock, rep1

description: Astrocytes, mock, rep1

value: mock


title: HAP, PBRM1KO, IFNg, Rep1


title: gq_sample_123

value: Peripheral blood

value: Duloxetine


title: YUMM-2w-Ctrl-0-n3

value: BSA (0 IU/mL)

value: 2 week and 0 hour


title: 5 weeks Astrocytes, cuprizone, rep3

description: Astrocytes, cuprizone, rep3

value: Brain

value: Rep 3


title: gq_sample_122

value: Week 8 Responder


title: YUMM-2w-Ctrl-0-n2


title: gq_sample_121

value: Placebo

value: Week 8 Non-Responder


title: 5 weeks Astrocytes, cuprizone, rep2

description: Astrocytes, cuprizone, rep2

value: Astrocytes

value: 5 weeks

value: Rep 2


title: HAP, wild-type, IFNg, Rep1

value: myeloid leukemia cells

value: IFNg treated


title: YUMM-2w-Ctrl-0-n1

value: Skin


title: HAP, PBRM1KO, untreated, Rep3

value: untreated


title: gq_sample_120


title: YUMM-1w-IFNg-24-n3

value: Melanoma

value: IFNG (50 IU/mL)

value: 1 week and 24 hour


title: HAP, PBRM1KO, untreated, Rep2


title: gq_sample_12

value: Peripheral blood

value: Duloxetine

value: Week 0 Responder


title: HAP, wild-type, IFNg, Rep3


title: gq_sample_119


title: HAP, wild-type, IFNg, Rep2


title: Ileum, 12 days after first switch, sample #3

value: Ileum

value: 12 days after first switch

value: regular diet


title: YUMM-1w-IFNg-24-n2


title: Ileum, 12 days after first switch, sample #2


title: HAP, wild-type, untreated, Rep2


title: gq_sample_117

value: Placebo

value: Week 8 Responder


title: Ileum, 9 days after first switch, sample #3

value: 9 days after first switch

value: feast diet


title: YUMM-1w-IFNg-2-n3

value: 1 week and 2 hour


title: Ileum, 12 days after first switch, sample #1


title: gq_sample_118

value: Week 8 Non-Responder


title: gq_sample_116


title: YUMM-1w-IFNg-2-n2

value: Skin


title: Ileum, 9 days after first switch, sample #2


title: YUMM-1w-IFNg-2-n1


title: YUMM-1w-IFNg-24-n1


title: HAP, wild-type, untreated, Rep1

value: myeloid leukemia cells

value: untreated


title: 5 weeks Astrocytes, cuprizone, rep1

description: Astrocytes, cuprizone, rep1

value: Brain

value: Astrocytes

value: GFAP-Cre+/- Rpl22HA/wt

value: cuprizone

value: 5 weeks

value: Rep 1


title: YUMM-1w-IFNg-0-n3

value: Melanoma

value: IFNG (50 IU/mL)

value: 1 week and 0 hour


title: Ileum, 9 days after first switch, sample #1

value: Ileum


title: gq_sample_115

value: Peripheral blood

value: Duloxetine


title: HAP1, IFNg, Pbrm1, Bethyl

data_processing:
ChIP-seq reads were QC-ed using fastqc version 0.11.5.
ChIP-seq reads were then aligned to the UCSC hg19 genome using Bowtie2 version 2.3.4.3 with default parameters for paired-end reads.
Then bam files were then filtered, sorted and indexed using samtools version 1.3.1. Dowstream processing and visualization was performed using deeptools version 3.5.0.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were normalized (to reads per million, rpm or bin per million) and reformatted in the bigWig file format.
Peaks were called uing MACS2 version 2.2.7.1. bigWig files were generated using deeptools version 3.5.0. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2.2.7.1 with the significance cut-off q-value 1.00e-03 and --nomodel.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Chromatin immunoprecipitation was performed as described (Miller EL et al. Nat Struct Mol Biol. 2017;24:344–52). Briefly, 10-30 million cells were cross-linked with 1% formaldehyde for 12 mins for room temperature, followed by  quenching with 125 mM glycine for 10 mins, washed with PBS, pelleted and flash-frozen.
Nuclei were isolated, rinsed and sonicated using an E220 Covaris sonicator, and the supernatant was used for immunoprecipitation with the indicated antibody. Antibodies used were anti-Pbrm1 (Bethyl, catalogue no. A301-590A and Novus Biologicals, catalogue no. NB100-79832). ChIP-sequencing libraries were prepared using Swift 2S ligation kit according to standard protocols and sequenced to a minimum of 40 million 150 bp read pairs each sample.
ChIP-seq libraries were prepared using Swift 2S ligation kit according to standard protocols.

treatment_protocol: For untreated cells, wild-type HAP1 cells were harvested and processed as described below. For IFN-γ treatment, HAP1 cells were treated with 50 ug/mL IFN-γ for 5 days. Medium was refreshed with cytokines at day 2-3.

value: Myeloid leukemia


title: gq_sample_114

value: Week 8 Responder


title: HAP, PBRM1KO, untreated, Rep1


title: YUMM-1w-IFNg-0-n2

value: Skin


title: HAP, wild-type, untreated, Rep3

value: myeloid leukemia cells


title: Ileum, 6 days after first switch, sample #2

value: 6 days after first switch

value: regular diet


title: YUMM-1w-IFNg-0-n1


title: HAP1, Untreated, Pbrm1, Bethyl


title: Ileum, 6 days after first switch, sample #3


title: Ileum, 6 days after first switch, sample #1


title: gq_sample_112

value: Placebo

value: Week 0 Non-Responder


title: HAP1, IFNg, Pbrm1, Novus


title: gq_sample_113

value: Week 0 Responder


title: gq_sample_110

value: Week 8 Non-Responder


title: YUMM-1w-Ctrl-0-n3

value: BSA (0 IU/mL)


title: Ileum, 3 days after first switch, sample #2

value: 3 days after first switch

value: feast diet


title: Ileum, 3 days after first switch, sample #3


title: gq_sample_111


title: YUMM-1w-Ctrl-0-n2

value: Melanoma

value: 1 week and 0 hour


title: HAP1, Input


title: OA_low (biol rep 2)

city: Frankfurt am Main

first: Martin

last: Wegner

state: Hessen

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry II

institute: University Hospital Frankfurt am Main, Germany

data_processing:
NextSeq Control Software 2.0.0
Adapter trimming: cutadapt v1.15 --pair-filter=any --minimum-length 20 --discard-untrimmed --max-n 0 --nextseq-trim=20 -e 0.1 -g TTGGGTACCTCG -G GACGAAACACCG
gRNA alignment: bowtie2 2.3.0 ..local -L11 -N 1 -i S,1.0,0.75
Supplementary files format and content: MTH01_DFPlow_R1.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_OAhigh_R3.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_OAhigh_R2.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_DFPhigh_R1.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_Library.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_D0_R2.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_D14_R1.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_D0_R1.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_DFPhigh_R3.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_OAlow_R1.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_DFPlow_R2.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_D0_R3.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_D14_R2.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_DFPlow_R3.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_OAlow_R3.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_OAlow_R2.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_DFPhigh_R2.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_D14_R3.csv table containing gRNA pairs and their abundance
Supplementary files format and content: MTH01_OAhigh_R1.csv table containing gRNA pairs and their abundance

source_name: Blood

extract_protocol: custom protocol for gDNA Isolation and PCR for amplification and barcoding

treatment_protocol: Mitophagy was induced at Day 14 by deferiprone (DFP) treatment or oligomycin/antimycin A (OA) treatment

value: Blood

value: acute monocytic leukemia

value: 10 µM OA 4h sorted LOW Mitophagy


title: gq_sample_11

value: Peripheral blood

value: Duloxetine


title: OA_low (biol rep 3)


title: Ileum, 0 days after first switch, sample #3

value: Ileum

value: 0 days after first switch


title: gq_sample_109

value: Week 8 Responder


title: HAP1, Untreated, Pbrm1, Novus

value: Myeloid leukemia


title: YUMM-0w-IFNg-24-n3

value: Skin

value: IFNG (50 IU/mL)

value: 0 week and 24 hour


title: OA_high (biol rep 3)

value: 10 µM OA 4h sorted HIGH Mitophagy


title: gq_sample_108

value: Week 0 Responder


title: YUMM-0w-IFNg-24-n1


title: Ileum, 0 days after first switch, sample #2

value: regular diet


title: OA_high (biol rep 2)


title: gq_sample_107

value: Placebo

value: Week 8 Non-Responder


title: YUMM-1w-Ctrl-0-n1

value: Melanoma

value: BSA (0 IU/mL)

value: 1 week and 0 hour


title: Ileum, 0 days after first switch, sample #1


title: YUMM-0w-IFNg-2-n3

value: 0 week and 2 hour


title: Ileum, 3 days after first switch, sample #1

value: 3 days after first switch

value: feast diet


title: OA_high (biol rep 1)

value: Blood

value: acute monocytic leukemia


title: Peyer's Patches, 12 days after first switch, sample #3

source_name: Peyer's Patches

value: Peyer's Patches

value: 12 days after first switch


title: Peyer's Patches, 12 days after first switch, sample #2


title: YUMM-0w-IFNg-2-n2

value: Skin

value: IFNG (50 IU/mL)


title: OA_low (biol rep 1)

value: 10 µM OA 4h sorted LOW Mitophagy


title: YUMM-0w-IFNg-2-n1


title: DFP_low (biol rep 3)

value: 0.5 mM DFP 16h sorted LOW mitophagy


title: gq_sample_104

value: Peripheral blood


title: gq_sample_105

value: Duloxetine


title: DFP_low (biol rep 1)


title: DFP_low (biol rep 2)


title: YUMM-0w-Ctrl-0-n3

value: 0 week and 0 hour


title: YUMM-0w-IFNg-24-n2

value: Melanoma

value: 0 week and 24 hour


title: gq_sample_103

value: Placebo

value: Week 8 Non-Responder


title: Peyer's Patches, 12 days after first switch, sample #1

value: regular diet


title: YUMM-0w-Ctrl-0-n2

value: BSA (0 IU/mL)


title: DFP_high (biol rep 3)

value: Blood

value: 0.5 mM DFP 16h sorted HIGH mitophagy


title: gq_sample_102


title: Peyer's Patches, 9 days after first switch, sample #2

value: Peyer's Patches

value: 9 days after first switch

value: feast diet


title: YUMM-0w-Ctrl-0-n1

value: Skin


title: DFP_high (biol rep 2)

value: acute monocytic leukemia


title: gq_sample_101

value: Week 0 Non-Responder


title: gq_sample_106

value: Peripheral blood


title: CT26-3w-IFNg-24-n3

source_name: Colon

value: Colon

value: Colorectal cancer

value: IFNG (50 IU/mL)

value: 3 week and 24 hour


title: gq_sample_100

value: Placebo


title: DFP_high (biol rep 1)


title: CT26-3w-IFNg-24-n2


title: Peyer's Patches, 6 days after first switch, sample #2

value: 6 days after first switch


title: CT26-3w-IFNg-24-n1


title: gq_sample_1

value: Week 0 Responder


title: Peyer's Patches, 9 days after first switch, sample #3


title: Peyer's Patches, 6 days after first switch, sample #1

value: regular diet


title: Day 14  (biol rep 2)

value: Blood

value: untreated  Day 14


title: gq_sample_10

value: Duloxetine


title: GRKO-Dexa-rep3

value: GRKO

value: 100nM Dexamethasone

value: 8 hours


title: Peyer's Patches, 3 days after first switch, sample #3

value: Peyer's Patches

value: 3 days after first switch

value: feast diet


title: CT26-3w-IFNg-2-n2

value: Colon

value: 3 week and 2 hour


title: Day 14  (biol rep 1)

value: acute monocytic leukemia


title: Day 0 (biol rep 3)

value: untreated Day 0


title: CT26-3w-IFNg-2-n3

value: Colorectal cancer

value: IFNG (50 IU/mL)


title: GRKO-Dexa-rep2


title: CT26-3w-IFNg-2-n1


title: Peyer's Patches, 3 days after first switch, sample #2


title: GRKO-Dexa-rep1


title: Day 0 (biol rep 2)


title: Peyer's Patches, 3 days after first switch, sample #1


title: Peyer's Patches, 9 days after first switch, sample #1

value: 9 days after first switch


title: CT26-3w-IFNg-0-n3

value: 3 week and 0 hour


title: GRKO-DMSO-rep3

value: DMSO


title: Day 0 (biol rep 1)

value: Blood


title: Peyer's Patches, 6 days after first switch, sample #3

value: 6 days after first switch

value: regular diet


title: Peyer's Patches, 0 days after first switch, sample #3

value: 0 days after first switch


title: Day 14  (biol rep 3)

value: untreated  Day 14


title: GRKO-DMSO-rep2

value: GRKO

value: 8 hours


title: CT26-3w-IFNg-0-n2


title: RKO-3

city: shanghai

first: Kong

last: Cheng

address: 270 Dong 'an Road

country: China

institute: fudan university shanghai cancer center

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: GRCh38 ensembl v101
Supplementary files format and content: FPKM values for each Sample

source_name: CRC cell lines

growth_protocol: Two CRC cell lines (HCT116, and RKO) were purchased from the American Type Culture Collection. The cell lines were verified by short-tandem repeat analysis and cultured in modified DMEM containing 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were exposed to PAA for 24 hours according the experiments. Regular medium with 0.1% DMSO was used as vehicle control.

value: CRC cell lines

value: RKO


title: Peyer's Patches, 0 days after first switch, sample #2

value: Peyer's Patches


title: RKO-2


title: CT26-3w-IFNg-0-n1

value: Colon


title: PAXIP1KO-2-Dexa-rep3

value: 100nM Dexamethasone


title: RKO-P3

value: PAA


title: Peyer's Patches, 0 days after first switch, sample #1


title: FACS-sorted CD4+Foxp3- T cells from Peyer's Patches, feast diet #2

source_name: CD4 T-cells from Peyer's Patches

extract_protocol:
Peyer’s patches (PPs) were removed from small intestine (SI) and put in TriFastTM (PeqLab, Cat.Nr.: 30-2010). Total RNA was purified using the NucleoSpin RNA II kit (Macherey & Nagel), according to manufacturer’s instructions. RNA sequencing was performed on FACS-sorted CD4+Foxp3- or CD45.1+ OT-II viable T cells isolated from PPs or dLN, respectively.
For library preparation of total PPs and ileum samples, cDNA was used as input to construct 250~300 bp insert cDNA libraries using NEBNext® UltraTM RNA Library Prep Kit (New England Biolabs, Ipswich, USA). Indices were included to multiplex multiple samples. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. For FACS-sorted cells, total RNA was amplified using SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing (Takara Bio USA, Inc., Mountain View, USA) with the double strand cDNA (ds-cDNA) being synthesized. Then ds-cDNA was purified with AMPure XP beads and quantified with Qubit (Life TechnologiesTM).  The library was ready after end repair, A-tailing, adapter ligation, and size selection. After amplification and purification, insert size of the library was validated on an Agilent 2100 and quantified using quantitative PCR (Q-PCR).

value: CD4 T-cells from Peyer's Patches

value: 3 days after switch to fest diet

value: feast diet


title: PAXIP1KO-2-Dexa-rep2


title: CT26-3w-Ctrl-0-n2

value: Colorectal cancer

value: BSA (0 IU/mL)

value: 3 week and 0 hour


title: CT26-3w-Ctrl-0-n1


title: RKO-P2


title: PAXIP1KO-2-Dexa-rep1


title: CT26-3w-Ctrl-0-n3


title: RKO-P1


title: CT26-2w-IFNg-24-n3

value: IFNG (50 IU/mL)

value: 2 week and 24 hour


title: FACS-sorted CD4+Foxp3- T cells from Peyer's Patches, feast diet #1


title: PAXIP1KO-2-DMSO-rep3

value: DMSO


title: GRKO-DMSO-rep1

value: GRKO


title: FACS-sorted CD4+Foxp3- T cells from Peyer's Patches, regular diet #2

value: on continuous regular diet

value: regular diet


title: HCT-116-3

value: CRC cell lines


title: CT26-2w-IFNg-24-n2


title: PAXIP1KO-2-DMSO-rep2

value: 8 hours


title: FACS-sorted CD4+Foxp3- T cells from Peyer's Patches, regular diet #1


title: CT26-2w-IFNg-24-n1

value: Colon


title: HCT-116-1


title: PAXIP1KO-2-DMSO-rep1


title: CT26-2w-IFNg-2-n3

value: 2 week and 2 hour


title: CD45.1+ OT-II viable T cells from dLN, feast diet #2

source_name: CD4 T-cells from dLN

value: CD4 T-cells from dLN

value: 5 days after switch to fest diet


title: HCT-116-P3

value: PAA


title: PAXIP1KO-1-Dexa-rep3

value: 100nM Dexamethasone


title: PAXIP1KO-1-Dexa-rep2


title: CT26-2w-IFNg-2-n2

value: Colorectal cancer


title: HCT-116-P2


title: FACS-sorted CD4+Foxp3- T cells from Peyer's Patches, regular diet #3

value: CD4 T-cells from Peyer's Patches


title: CD45.1+ OT-II viable T cells from dLN, feast diet #1

value: feast diet


title: PAXIP1KO-1-Dexa-rep1


title: CT26-2w-IFNg-2-n1

value: IFNG (50 IU/mL)


title: CD45.1+ OT-II viable T cells from dLN, regular diet #2


title: CT26-2w-IFNg-0-n2

value: 2 week and 0 hour


title: HC Blood, CD1a_GAS, 6 hr 2

city: Oxford

first: Yi-Ling

last: Chen

state: Oxfordshire

address: Old Road Campus

department: Nuffield Department of Medicine

country: United Kingdom

institute: CAMS Oxford Institute (COI)

description:
10x Genomics
Feature Barcode

data_processing:
For each sequenced scRNA-Seq pool, Cell Ranger toolkit (version 6.0.1) was used to process raw data, map cDNA libraries against hg38 human reference genome from the UCSC ftp site and to summarize unique molecular identifier (UMI) counts against the corresponding Ensemble gene annotations.
Further processing was done with Seurat v4.1.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include counts and matrix files

growth_protocol: CD3+ cells were MACS separated from skin mononuclear cells or PBMCs, and rested in RPMI medium containing 200 U/ml IL-2+8% Human serum for 3 days.

extract_protocol:
Samples were subjected to Cytokine secretion assay and then stained with fluorochrome-conjugated anti-CD3 antibody, TotalSeq-C antibody cocktail and a unique hashtag for each sample. Samples were washed, pooled and CD3+ T cells were FACS-sorted. The target cells were loaded into a Chromium Controller (10X Genomics).
Libraries were prepared with the Chromium Single Cell 5’ Library & Gel Bead Kit v1.1. Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the manufacturer’s protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). We further proceeded according to the manufacturer’s instructions for Cell Surface Protein/Immune Receptor Mapping Libraries and 5ʹ Gene Expression (GEX) Libraries.
scRNA-seq
CITE-seq

treatment_protocol: Rested T cells were co-cultured with K562-CD1a or K562-CD1a infected with GAS for 6 hours

value: Blood

value: primary

value: CD3+ T cells


title: CD45.1+ OT-II viable T cells from dLN, regular diet #1

value: on continuous regular diet

value: regular diet


title: HC Blood, CD1a_GAS, 6 hr 1

description:
10x Genomics
total RNA

library_source: transcriptomic single cell


title: PAXIP1KO-1-DMSO-rep2

value: DMSO

value: 8 hours


title: Peyer's Patches, feast diet, sample #3

value: Peyer's Patches


title: CT26-2w-IFNg-0-n1

value: Colon


title: HCT-116-2

value: CRC cell lines


title: PAXIP1KO-1-DMSO-rep1


title: HC Blood, Unstimulated 2

description:
10x Genomics
Feature Barcode

value: Unstimulated


title: CT26-2w-Ctrl-0-n3

value: BSA (0 IU/mL)


title: Peyer's Patches, feast diet, sample #1


title: Peyer's Patches, feast diet, sample #2


title: HC Blood, Unstimulated 1

description:
10x Genomics
total RNA


title: Peyer's Patches, regular diet, sample #3


title: CT26-2w-Ctrl-0-n2

value: Colorectal cancer


title: NT-1-Dexa-rep3

value: 100nM Dexamethasone


title: HC Blood, CD1a_auto, 6 hr 2

description:
10x Genomics
Feature Barcode


title: NT-1-Dexa-rep2


title: Peyer's Patches, regular diet, sample #2


title: HCT-116-P1

value: PAA


title: HC Blood, CD1a_auto, 6 hr 1

description:
10x Genomics
total RNA


title: PAXIP1KO-1-DMSO-rep3


title: CT26-2w-IFNg-0-n3

value: IFNG (50 IU/mL)


title: NT-1-Dexa-rep1


title: CT26-2w-Ctrl-0-n1

value: 2 week and 0 hour


title: Peyer's Patches, regular diet, sample #1


title: HC Blood, CD1a_auto_GAS, 6 hr 2

description:
10x Genomics
Feature Barcode

value: Blood


title: CT26-1w-IFNg-24-n3

value: 1 week and 24 hour


title: M3_repl3

city: Seattle

first: Asia

last: Mendelevich

state: WA

address: 2211 Elliott Ave

institute: Altius

description:
Abl. 1 cell line (129S1xCAST F1), biological replicate 3, library preparation replicate 3
LOVSON_E1.Mouse_only.counts.tsv

data_processing:
Sequence reads were aligned on two alellic pseudogenomes using STAR v2.7.9a (with parameters –outSAMattributes vA vG).
Uniquely aligned reads were assigned towards one of the alleles according to their SNP calls and alignment quality (see https://github.com/gimelbrantlab/fastq2allelictabs).
Allelic gene counts were calculated using featurecounts v2.0.2.
Supplementary files format and content: Tab-delimited text files include allelic gene count values for each sample.

source_name: v-Abl pro-B clonal cell line Abl.1

extract_protocol:
Agilent Mini
NEBNext® Single Cell/Low Input RNA

value: v-Abl pro-B clonal cell line Abl.1

value: pro-B cells

value: WT

tag: strain

value: 129S1/SvImJ x Cast/EiJ F1


title: CT26-1w-IFNg-24-n1


title: M3_repl2

description:
Abl. 1 cell line (129S1xCAST F1), biological replicate 3, library preparation replicate 2
LOVSON_E1.Mouse_only.counts.tsv


title: NT-1-DMSO-rep2

value: DMSO

value: 8 hours


title: CT26-1w-IFNg-24-n2

value: Colon


title: NT-1-DMSO-rep1


title: HC Skin_CD1a_GAS, 6 hr 4

description:
10x Genomics
Feature Barcode

value: Skin

value: primary

value: CD3+ T cells


title: M3_repl1

description:
Abl. 1 cell line (129S1xCAST F1), biological replicate 3, library preparation replicate 1
LOVSON_E1.Mouse_only.counts.tsv


title: CT26-1w-IFNg-2-n3

value: Colorectal cancer

value: 1 week and 2 hour


title: HC Skin_CD1a_GAS, 6 hr 3

description:
10x Genomics
total RNA


title: M2_repl3

description:
Abl. 1 cell line (129S1xCAST F1), biological replicate 2, library preparation replicate 3
LOVSON_E1.Mouse_only.counts.tsv


title: CT26-1w-IFNg-2-n2


title: A549-PAXIP1KO-rep2+Dex(100nM) [RAD21_8]

value: Lung Cancer

value: 100nM Dexamethasone


title: A549-PAXIP1KO-rep1+Dex(100nM) [RAD21_7]


title: M2_repl2

description:
Abl. 1 cell line (129S1xCAST F1), biological replicate 2, library preparation replicate 2
LOVSON_E1.Mouse_only.counts.tsv


title: CT26-1w-IFNg-2-n1

value: IFNG (50 IU/mL)


title: NT-1-DMSO-rep3


title: HC Skin_CD1a_GAS, 6 hr 1

description:
10x Genomics
total RNA


title: A549-PAXIP1KO-rep1-vhcl [RAD21_5]


title: M1_repl3

description:
Abl. 1 cell line (129S1xCAST F1), biological replicate 1, library preparation replicate 3
LOVSON_E1.Mouse_only.counts.tsv


title: HC_PS Blood_Unstimulated 2

description:
10x Genomics
Feature Barcode

value: Unstimulated


title: CT26-1w-IFNg-0-n2

value: 1 week and 0 hour


title: CT26-1w-IFNg-0-n3


title: M1_repl2

description:
Abl. 1 cell line (129S1xCAST F1), biological replicate 1, library preparation replicate 2
LOVSON_E1.Mouse_only.counts.tsv

value: v-Abl pro-B clonal cell line Abl.1


title: M2_repl1

description:
Abl. 1 cell line (129S1xCAST F1), biological replicate 2, library preparation replicate 1
LOVSON_E1.Mouse_only.counts.tsv

value: pro-B cells


title: HC Blood, CD1a_auto_GAS, 6 hr 1

description:
10x Genomics
total RNA

value: Blood


title: A549-PAXIP1KO-rep2-vhcl [RAD21_6]


title: M1_repl1

description:
Abl. 1 cell line (129S1xCAST F1), biological replicate 1, library preparation replicate 1
LOVSON_E1.Mouse_only.counts.tsv

value: WT

value: 129S1/SvImJ x Cast/EiJ F1


title: A549-NT(1)-rep1+Dex(100nM) [RAD21_3]


title: HC Skin_CD1a_GAS, 6 hr 2

description:
10x Genomics
Feature Barcode


title: HC_PS Blood_CD1a_GAS_6 hr, HC Skin_Unstimulated 2

description:
10x Genomics
Feature Barcode

source_name: Skin/blood

value: Skin/blood


title: CT26-1w-IFNg-0-n1

value: Colon


title: HC_PS Blood_Unstimulated 1

description:
10x Genomics
total RNA

value: Skin


title: HC_PS Blood_CD1a_GAS_6 hr, HC Skin_Unstimulated 1

description:
10x Genomics
total RNA

value: primary


title: CT26-1w-Ctrl-0-n3

value: BSA (0 IU/mL)


title: A549-NT(1)-rep2-vhcl [RAD21_2]

value: DMSO


title: CT26-1w-Ctrl-0-n2

value: Colorectal cancer


title: HC_PS Blood_CD1a_auto, HC Skin_CD1a_GAS, 6 hr 2

description:
10x Genomics
Feature Barcode

value: CD3+ T cells


title: A549-NT(1)-rep1-vhcl [RAD21_1]

value: Lung Cancer


title: HC_PS Blood_CD1a_auto, HC Skin_CD1a_GAS, 6 hr 1

description:
10x Genomics
total RNA


title: AML, Tet2Tet3Pbrm1, Rep4

data_processing:
Sequence reads were QC-ed using fastqc version 0.11.3.
Sequence reads were mapped to mm9 using STAR aligner version 2.5.2b with default parameters. Gene counts were generated using featureCounts version 2.0.1 with default parameters. Gene counts were then extracted and merged to obtain final raw counts for each gene across samples.
Normalization and the discovery of differentially expressed genes were performed using DESeq2 version 1.34.0 in R 4.1.2 with default parameters.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: Bone marrow

extract_protocol:
Blasts from bone marrow of leukemic mice were processed into single cell suspension and enumerated from each biological replicate. RNA from roughly about 1 million cells were harvested using RNeasy Mini Plus kit (Qiagen). The resultant RNA were Dnase-treated and 200 ng RNA were used for subsequent enrichment and library preparation.
RNA-seq libraries were prepared from poly-A-enriched mRNA using a KAPA mRNA HyperPrep Kit (Roche) and sequenced on an Illumina Novaseq.

value: Bone marrow

value: myeloid leukemia cells


title: A549-STAG-2-mixed input  [GR_28]

value: mixed


title: CT26-1w-Ctrl-0-n1

value: 1 week and 0 hour


title: SOCS3WT_KO_Tcells_scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
MC38 tumor mass were excised and minced and digested with 0.25% Liberase TM (Merck) and 20 kU/mL DNase I (Sigma-Aldrich, St Louis, MO) at 37 °C for 30 minutes with gentle shaking. Cells were passed through a 100-μm filter and subjected to 40% Percoll centrifugation to remove debris and epithelial cells from the surface of the solution. Red blood cell lysis was performed if necessary, and the cells were washed twice with phosphate-buffered saline (PBS). The cells were incubated with anti-CD3e+-Brilliant violet-421 , anti-TCRb+-APC antibodies, and Fixable viabily dye -eFlour 780 in the presence of TotalSeq -C0301, C0302, C0303 or C0304 anti-mouse Hashtag antibodies in each mouse sample. CD3e+ TCRb+ cells were isolated by FACS AriaIII.
Library was performed according to the manufacter’s instructions (Chromium Next GEM SIngle Cell 5'Reagent Kits v2, 10x Genomics). Briefly, T cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was reversely transcribed to cDNA with Gel Bead primers containingan Illumina TruSeq Read1 sequence, a  10x Barcode, a unique Molecular Identifier (UMI), and template switch oligo (TSO), and poly(dT) primers.  Simultaneously in the same partition, the Gel Bead primer captures the cell surface protein Feature Barcode conjugated to HashTag antibodies containing a Nextera Read 2 , a Feature Barcode, and capture sequence, and produces 10x Barcoded DNA with Feature Barcode of Hash Tag antibodies. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R1 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: MC38 (2 x 10^6 cells/mouse) were subcutaneously inoculated into the right flank of two WT Socs3f/f and two Cd4Cre Socs3f/f mice. On day 12, the CD3e and TCRb+ cells of tumor tissue from each implanted mouse were used as a single-cell RNA sequencing sample.

value: MC38 tumor

value: T cells

value: TIL

value: WT & SOCS3KO

value: no treatment


title: AML, Tet2Tet3Pbrm1, Rep3


title: CT26-0w-IFNg-24-n3

value: Colon

value: IFNG (50 IU/mL)

value: 0 week and 24 hour


title: A549-NT(1)-rep2+Dex(100nM) [RAD21_4]

value: 100nM Dexamethasone


title: A549-NT(2)-mixed input [GR_27]


title: AML, Tet2Tet3Pbrm1, Rep2


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 2, channel 4, sgRNA

city: London

first: Simon

last: Butterworth

address: 1 Midland Road

institute: The Francis Crick Institute

description:
10x Genomics Feature Barcode for CRISPR screening library, dual index
BUT290A51_BUT290A52_matrix.mtx.gz
BUT290A51_BUT290A52_barcodes.tsv.gz
BUT290A51_BUT290A52_features.tsv.gz

library_source: other

data_processing:
A custom dual reference for Homo sapiens GRCh38 Ensembl release 95 and Toxoplasma gondii ME49 TGA4 Ensembl Protists release 42 was generated using Cell Ranger v3.0.2 (10x Genomics) mkref for multiple species.
Pre-processing of fastq data to generate count matrices was carried out using Cell Ranger Cell Ranger v6.1.2 (10x Genomics) count with the above dual reference genome and using --include-introns flag, the --libraries flag to specify samples as "Gene Expression" or "CRISPR Guide Capture," and the --feature-ref flag to pass a custom reference of sgRNA protospacer sequences and identities.
Further data analysis using the count matrices was carried out in R v4.0.2 using Seurat v4.2.0.
Assembly: GRCh38, TGA4
Supplementary files format and content: Cell Ranger output files in "filtered_feature_bc_matrix": barcodes.tsv barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: other

organism:
Toxoplasma gondii
Homo sapiens

source_name: Human foreskin fibroblast (HFF)

growth_protocol:
HFFs were grown to confluence in DMEM with high glucose and GlutaMAX plus 10% heat-inactivated FBS.
Toxoplasma gondii CRISPR mutants were generated by transfection with a linearised Cas9-sgRNA vector by electroporation and selected for integration of this vector for at least six days during serial passage in HFFs.

extract_protocol:
24 hours post-infection, the HFFs were dissociated with TrypLE Express and infected cells were enriched by fluorescence activated cell sorting. Sorted cells were concentrated by centrifugation, resuspended in PBS with 0.04% BSA, and cell number and viability checked using an automated cell counter. Cells wereloaded into a 10x Genomics Chromium Controller with a targeted recovery of 10,000 cells per channel.
Libraries were constructed according to 10x Genomics user guides CG000389 (for single index samples) or CG000316 (for dual index samples): Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 with Feature Barcode technology for CRISPR Screening

treatment_protocol:
Confluent HFFs were infected with Toxoplasma gondii CRISPR mutants for 24 h at a multiplicity of infection of 0.1.
For interferon-gamma treated samples, recombinant human interferon-gamma was added at 21 hours post-infection to a final concentration of 5 ng/mL (~10 U/mL).

value: Human foreskin fibroblast (HFF)

tag: infection

value: Infected with Toxoplasma gondii RH CRISPR mutants for 24 h

value: Interferon-gamma stimulated

tag: library type

value: CRISPR sgRNA


title: CT26-0w-IFNg-24-n2

value: Colorectal cancer


title: A549-PAXIP1-KO-mixed input [GR_26]

value: Lung Cancer


title: AML, Tet2Tet3Pbrm1, Rep1

value: Bone marrow

value: myeloid leukemia cells


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 2, channel 4, mRNA

description:
10x Genomics 3' v3 mRNA library, dual index
BUT290A51_BUT290A52_matrix.mtx.gz
BUT290A51_BUT290A52_barcodes.tsv.gz
BUT290A51_BUT290A52_features.tsv.gz

value: mRNA


title: CT26-0w-IFNg-24-n1


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 2, channel 3, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, dual index
BUT290A49_BUT290A50_matrix.mtx.gz
BUT290A49_BUT290A50_barcodes.tsv.gz
BUT290A49_BUT290A50_features.tsv.gz


title: A549-NT(1)-mixed input [GR_25]

value: mixed


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 2, channel 3, mRNA

description:
10x Genomics 3' v3 mRNA library, dual index
BUT290A49_BUT290A50_matrix.mtx.gz
BUT290A49_BUT290A50_barcodes.tsv.gz
BUT290A49_BUT290A50_features.tsv.gz


title: CT26-0w-IFNg-2-n3

value: 0 week and 2 hour


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 2, channel 2, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, dual index
BUT290A47_BUT290A48_matrix.mtx.gz
BUT290A47_BUT290A48_barcodes.tsv.gz
BUT290A47_BUT290A48_features.tsv.gz


title: A549-STAG2KO-rep3+Dex(100nM) [GR_24]

value: GR (12041, Cell Signaling Technology)


title: AML, Tet2Tet3, Rep4


title: CT26-0w-IFNg-2-n2


title: AML, Tet2Tet3, Rep3


title: CT26-0w-IFNg-2-n1


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 2, channel 2, mRNA

description:
10x Genomics 3' v3 mRNA library, dual index
BUT290A47_BUT290A48_matrix.mtx.gz
BUT290A47_BUT290A48_barcodes.tsv.gz
BUT290A47_BUT290A48_features.tsv.gz


title: CT26-0w-Ctrl-0-n3

value: BSA (0 IU/mL)

value: 0 week and 0 hour


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 2, channel 1, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, dual index
BUT290A45_BUT290A46_matrix.mtx.gz
BUT290A45_BUT290A46_barcodes.tsv.gz
BUT290A45_BUT290A46_features.tsv.gz


title: A549-STAG2KO-rep1+Dex(100nM) [GR_22]


title: A549-STAG2KO-rep3-vhcl [GR_21]

value: DMSO


title: AML, Tet2Tet3, Rep2


title: CT26-0w-Ctrl-0-n2

value: Colon


title: AML, Tet2Tet3, Rep1


title: Treg, TCR retaining, 21 days, rep2 [H29_pos]

city: La Jolla

first: Stanislav

last: Dikiy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

description: SMARTer Amp library

data_processing:
Adapter trimming: Trimmomatic (version 0.39): TrimmomaticPE Sample_R1.fastq.gz Sample_R2.fastq.gz -baseout Sample.fastq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignment: STAR (version 2.7.3a): STAR --runThreadN 6 --runMode alignReads --genomeLoad NoSharedMemory --readFilesCommand zcat --genomeDir mm39_100_RNA --readFilesIn Sample_1P.fastq.gz Sample_2P.fastq.gz --outFileNamePrefix Sample --outSAMtype BAM Unsorted --outBAMcompression 6 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.06 --outFilterMatchNminOverLread 0.35 --outFilterMatchNmin 60 --alignEndsType EndToEnd
Sort: samtools (version 1.12): samtools sort -@ 4 -n -o Sample.bam SampleAligned.out.bam
Mate coordinates: samtools (version 1.12): samtools fixmate -@ 4 -rm Sample.bam Sample.fixmate.bam
Sort: samtools (version 1.12): samtools sort -@ 4 -o Sample.resort.bam Sample.fixmate.bam
Remove duplicates: samtools (version 1.12): samtools markdup -@ 4 -l 1500 -r -d 100 -s Sample.resort.bam Sample.duprm.bam
Index: samtools (version 1.12): samtools index -@ 4 -b Sample.duprm.bam
Count reads: GenomicAlignments (R, version 1.26.0): summarizeOverlaps (default parameters)
Assembly: mm39 (custom with Foxp3, Il10, Trac, and Gt(ROSA)26Sor loci altered)
Supplementary files format and content: counts_TracRNA_AllSamples.txt: text file with all raw counts generated by GenomicAlignments summarizeOverlaps

extract_protocol:
Cells sorted directly into Trizol LS; phase separation was induced with 200 µL chloroform. RNA was extracted from 350 µL of the aqueous phase using the miRNeasy Micro Kit (Qiagen catalog # 217084) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol. Samples were eluted in 13 µL RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 122-400pg total RNA with RNA integrity numbers ranging from undetectable to 9 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 4ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run with the NovaSeq 6000 S4 Reagent Kit (Cycles), (Illumina).

treatment_protocol: Mice treated with tamoxifen 21 days prior to cell isolation to activate an Il10 linked CreER, inducing permanent YFP labeling of Il10 expressing cells and deletion of Trac in 30-60% of these cells

value: regulatory T cell

tag: mouse

tag: tcr cell_surface

value: Positive

tag: timepoint

value: 21 days


title: CT26-0w-Ctrl-0-n1

tag: tissue

tag: treatment


title: A549-STAG2KO-rep2-vhcl [GR_20]

tag: cell line


title: A549-STAG2KO-rep1-vhcl [GR_19]

tag: genotype


title: Treg, TCR retaining, 21 days, rep1 [H28_pos]

description: SMARTer Amp library


title: donor1_biorepl2_spikein_50pRNA_M

description:
donor no. 1 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 1 peripheral blood monocytes, biological replicate 2, with 50 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

organism:
Homo sapiens
Mus musculus

source_name: peripheral blood monocytes / pro-B cells

extract_protocol:
Qiagen Mini / Agilent Mini
SMART-Seq v4 PLUS kit (Takara)

value: WT

value: donor no. 1 / 129S1/SvImJ x Cast/EiJ F1


title: Dual perturb-seq screen, unstimulated, replicate 3, channel 4, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, dual index
BUT290A43_BUT290A44_matrix.mtx.gz
BUT290A43_BUT290A44_barcodes.tsv.gz
BUT290A43_BUT290A44_features.tsv.gz

value: Human foreskin fibroblast (HFF)

value: Infected with Toxoplasma gondii RH CRISPR mutants for 24 h

value: Unstimulated

value: CRISPR sgRNA


title: AML, Tet2Tet3, Rep5

value: Bone marrow

value: myeloid leukemia cells


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 2, channel 1, mRNA

description:
10x Genomics 3' v3 mRNA library, dual index
BUT290A45_BUT290A46_matrix.mtx.gz
BUT290A45_BUT290A46_barcodes.tsv.gz
BUT290A45_BUT290A46_features.tsv.gz

value: Interferon-gamma stimulated

value: mRNA


title: A549-PAXIP1KO-rep3+Dex(100nM) [GR_12]

value: Lung Cancer

value: 100nM Dexamethasone

value: GR (12041, Cell Signaling Technology)


title: Treg, TCR retaining, 10 days, rep2 [H32_pos]

description: SMARTer Amp library

value: Colon

value: 10 days


title: A549-STAG2KO-rep2+Dex(100nM) [GR_23]


title: Dual perturb-seq screen, unstimulated, replicate 3, channel 4, mRNA

description:
10x Genomics 3' v3 mRNA library, dual index
BUT290A43_BUT290A44_matrix.mtx.gz
BUT290A43_BUT290A44_barcodes.tsv.gz
BUT290A43_BUT290A44_features.tsv.gz


title: donor3_biorepl1_spikein_50pRNA_M

description:
donor no. 3 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 3 peripheral blood monocytes, biological replicate 1, with 50 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: peripheral blood monocytes / pro-B cells

value: donor no. 3 / 129S1/SvImJ x Cast/EiJ F1


title: Dual perturb-seq screen, unstimulated, replicate 3, channel 3, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, dual index
BUT290A41_BUT290A42_matrix.mtx.gz
BUT290A41_BUT290A42_barcodes.tsv.gz
BUT290A41_BUT290A42_features.tsv.gz


title: Dual perturb-seq screen, unstimulated, replicate 3, channel 3, mRNA

description:
10x Genomics 3' v3 mRNA library, dual index
BUT290A41_BUT290A42_matrix.mtx.gz
BUT290A41_BUT290A42_barcodes.tsv.gz
BUT290A41_BUT290A42_features.tsv.gz


title: Treg, TCR retaining, 10 days, rep1 [H31_pos]

description: SMARTer Amp library

value: regulatory T cell

value: Positive


title: donor1_biorepl1_spikein_50pRNA_M

description:
donor no. 1 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 1 peripheral blood monocytes, biological replicate 1, with 50 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: WT

value: donor no. 1 / 129S1/SvImJ x Cast/EiJ F1


title: Treg, TCR losing, 21 days, rep2 [H29_neg]

description: SMARTer Amp library

value: Negative

value: 21 days


title: donor2_biorepl1_spikein_50pRNA_M

description:
donor no. 2 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 2 peripheral blood monocytes, biological replicate 1, with 50 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: donor no. 2 / 129S1/SvImJ x Cast/EiJ F1


title: Treg, TCR losing, 21 days, rep1 [H28_neg]

description: SMARTer Amp library


title: Dual perturb-seq screen, unstimulated, replicate 3, channel 2, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, dual index
BUT290A39_BUT290A40_matrix.mtx.gz
BUT290A39_BUT290A40_barcodes.tsv.gz
BUT290A39_BUT290A40_features.tsv.gz

value: Human foreskin fibroblast (HFF)

value: Infected with Toxoplasma gondii RH CRISPR mutants for 24 h

value: Unstimulated

value: CRISPR sgRNA


title: Dual perturb-seq screen, unstimulated, replicate 3, channel 2, mRNA

description:
10x Genomics 3' v3 mRNA library, dual index
BUT290A39_BUT290A40_matrix.mtx.gz
BUT290A39_BUT290A40_barcodes.tsv.gz
BUT290A39_BUT290A40_features.tsv.gz

value: mRNA


title: A549-PAXIP1KO-rep3-vhcl [GR_9]

value: Lung Cancer

value: DMSO

value: GR (12041, Cell Signaling Technology)


title: donor1_biorepl2_spikein_25pRNA_M

description:
donor no. 1 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 1 peripheral blood monocytes, biological replicate 2, with 25 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: peripheral blood monocytes / pro-B cells


title: A549-PAXIP1KO-rep2-vhcl [GR_8]


title: Treg, TCR losing, 10 days, rep2 [H32_neg]

description: SMARTer Amp library

value: Colon

value: 10 days


title: donor3_biorepl1_spikein_25pRNA_M

description:
donor no. 3 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 3 peripheral blood monocytes, biological replicate 1, with 25 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: donor no. 3 / 129S1/SvImJ x Cast/EiJ F1


title: Dual perturb-seq screen, unstimulated, replicate 3, channel 1, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, dual index
BUT290A37_BUT290A38_matrix.mtx.gz
BUT290A37_BUT290A38_barcodes.tsv.gz
BUT290A37_BUT290A38_features.tsv.gz


title: A549-PAXIP1KO-rep1-vhcl [GR_7]


title: Dual perturb-seq screen, unstimulated, replicate 3, channel 1, mRNA

description:
10x Genomics 3' v3 mRNA library, dual index
BUT290A37_BUT290A38_matrix.mtx.gz
BUT290A37_BUT290A38_barcodes.tsv.gz
BUT290A37_BUT290A38_features.tsv.gz


title: donor1_biorepl1_spikein_25pRNA_M

description:
donor no. 1 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 1 peripheral blood monocytes, biological replicate 1, with 25 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: WT


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 1, channel 4, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, dual index
BUT290A35_BUT290A36_matrix.mtx.gz
BUT290A35_BUT290A36_barcodes.tsv.gz
BUT290A35_BUT290A36_features.tsv.gz

value: Interferon-gamma stimulated


title: Treg, TCR losing, 10 days, rep1 [H31_neg]

description: SMARTer Amp library

value: regulatory T cell

value: Negative


title: A549-PAXIP1KO-rep2+Dex(100nM) [GR_11]

value: 100nM Dexamethasone


title: A549-NT(1)-rep2+Dex(100nM) [GR_5]


title: WormMix_W3_techrepl3

description:
N2 and Hawaii strains
C.elegans strains (N2:Hawaii) RNA mix (1:3), library preparation replicate 3
STARA_E3.Roundworm_only.counts.tsv

organism: Caenorhabditis elegans

source_name: whole organism

extract_protocol:
Trizol
SMART-Seq v4 PLUS kit (Takara)

value: whole organism

value: N2 x Hawaii


title: A549-PAXIP1KO-rep1+Dex(100nM) [GR_10]


title: A549-NT(1)-rep1+Dex(100nM) [GR_4]


title: WormMix_W3_techrepl1

description:
N2 and Hawaii strains
C.elegans strains (N2:Hawaii) RNA mix (1:3), library preparation replicate 1
STARA_E3.Roundworm_only.counts.tsv


title: donor7_biorepl2_spikein_10pRNA_M

description:
donor no. 7 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 7 peripheral blood monocytes, biological replicate 2, with 10 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: donor no. 7 / 129S1/SvImJ x Cast/EiJ F1


title: donor2_biorepl1_spikein_25pRNA_M

description:
donor no. 2 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 2 peripheral blood monocytes, biological replicate 1, with 25 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: donor no. 2 / 129S1/SvImJ x Cast/EiJ F1


title: donor6_biorepl2_spikein_10pRNA_M

description:
donor no. 6 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 6 peripheral blood monocytes, biological replicate 2, with 10 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: donor no. 6 / 129S1/SvImJ x Cast/EiJ F1


title: WormMix_W2_techrepl3

description:
N2 and Hawaii strains
C.elegans strains (N2:Hawaii) RNA mix (3:1), library preparation replicate 3
STARA_E3.Roundworm_only.counts.tsv


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 1, channel 3, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, dual index
BUT290A33_BUT290A34_matrix.mtx.gz
BUT290A33_BUT290A34_barcodes.tsv.gz
BUT290A33_BUT290A34_features.tsv.gz

value: Human foreskin fibroblast (HFF)

value: Infected with Toxoplasma gondii RH CRISPR mutants for 24 h

value: CRISPR sgRNA


title: WormMix_W3_techrepl2

description:
N2 and Hawaii strains
C.elegans strains (N2:Hawaii) RNA mix (1:3), library preparation replicate 2
STARA_E3.Roundworm_only.counts.tsv


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 1, channel 4, mRNA

description:
10x Genomics 3' v3 mRNA library, dual index
BUT290A35_BUT290A36_matrix.mtx.gz
BUT290A35_BUT290A36_barcodes.tsv.gz
BUT290A35_BUT290A36_features.tsv.gz

value: mRNA


title: donor5_biorepl2_spikein_10pRNA_M

description:
donor no. 5 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 5 peripheral blood monocytes, biological replicate 2, with 10 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: peripheral blood monocytes / pro-B cells

value: donor no. 5 / 129S1/SvImJ x Cast/EiJ F1


title: A549-NT(1)-rep3-vhcl [GR_3]

value: Lung Cancer

value: DMSO

value: GR (12041, Cell Signaling Technology)


title: A549-NT(1)-rep2-vhcl [GR_2]


title: WormMix_W2_techrepl2

description:
N2 and Hawaii strains
C.elegans strains (N2:Hawaii) RNA mix (3:1), library preparation replicate 2
STARA_E3.Roundworm_only.counts.tsv

value: WT


title: donor4_biorepl2_spikein_10pRNA_M

description:
donor no. 4 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 4 peripheral blood monocytes, biological replicate 2, with 10 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: donor no. 4 / 129S1/SvImJ x Cast/EiJ F1


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 1, channel 3, mRNA

description:
10x Genomics 3' v3 mRNA library, dual index
BUT290A33_BUT290A34_matrix.mtx.gz
BUT290A33_BUT290A34_barcodes.tsv.gz
BUT290A33_BUT290A34_features.tsv.gz

value: Interferon-gamma stimulated


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 1, channel 2, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, dual index
BUT290A31_BUT290A32_matrix.mtx.gz
BUT290A31_BUT290A32_barcodes.tsv.gz
BUT290A31_BUT290A32_features.tsv.gz


title: donor7_biorepl1_spikein_10pRNA_M

description:
donor no. 7 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 7 peripheral blood monocytes, biological replicate 1, with 10 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv


title: WormMix_W2_techrepl1

description:
N2 and Hawaii strains
C.elegans strains (N2:Hawaii) RNA mix (3:1), library preparation replicate 1
STARA_E3.Roundworm_only.counts.tsv

value: whole organism


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 1, channel 2, mRNA

description:
10x Genomics 3' v3 mRNA library, dual index
BUT290A31_BUT290A32_matrix.mtx.gz
BUT290A31_BUT290A32_barcodes.tsv.gz
BUT290A31_BUT290A32_features.tsv.gz


title: A549-NT(1)-rep3+Dex(100nM) [GR_6]

value: 100nM Dexamethasone


title: donor1_biorepl2_spikein_50pRNA_W1

description:
donor no. 1 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 1 peripheral blood monocytes, biological replicate 2, with 50 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

organism:
Caenorhabditis elegans
Homo sapiens

source_name: peripheral blood monocytes / whole organism

extract_protocol:
Qiagen Mini / Trizol
SMART-Seq v4 PLUS kit (Takara)

value: donor no. 1 / N2 x Hawaii


title: WormMix_W1_techrepl3

description:
N2 and Hawaii strains
C.elegans strains (N2:Hawaii) RNA mix (1:1), library preparation replicate 3
STARA_E3.Roundworm_only.counts.tsv

value: N2 x Hawaii


title: donor6_biorepl1_spikein_10pRNA_M

description:
donor no. 6 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 6 peripheral blood monocytes, biological replicate 1, with 10 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: donor no. 6 / 129S1/SvImJ x Cast/EiJ F1


title: donor5_biorepl1_spikein_10pRNA_M

description:
donor no. 5 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 5 peripheral blood monocytes, biological replicate 1, with 10 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 1, channel 1, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, dual index
BUT290A29_BUT290A30_matrix.mtx.gz
BUT290A29_BUT290A30_barcodes.tsv.gz
BUT290A29_BUT290A30_features.tsv.gz

value: Human foreskin fibroblast (HFF)


title: WormMix_W1_techrepl2

description:
N2 and Hawaii strains
C.elegans strains (N2:Hawaii) RNA mix (1:1), library preparation replicate 2
STARA_E3.Roundworm_only.counts.tsv


title: donor1_biorepl1_spikein_50pRNA_W1

description:
donor no. 1 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 1 peripheral blood monocytes, biological replicate 1, with 50 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: peripheral blood monocytes / whole organism


title: WormMix_W1_techrepl1

description:
N2 and Hawaii strains
C.elegans strains (N2:Hawaii) RNA mix (1:1), library preparation replicate 1
STARA_E3.Roundworm_only.counts.tsv


title: donor4_biorepl1_spikein_10pRNA_M

description:
donor no. 4 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 4 peripheral blood monocytes, biological replicate 1, with 10 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv


title: Dual perturb-seq screen, unstimulated, replicate 2, channel 2, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, single index
BUT290A27_BUT290A28_matrix.mtx.gz
BUT290A27_BUT290A28_barcodes.tsv.gz
BUT290A27_BUT290A28_features.tsv.gz

value: Infected with Toxoplasma gondii RH CRISPR mutants for 24 h

value: Unstimulated

value: CRISPR sgRNA


title: donor1_biorepl3_spikein_10pRNA_M

description:
donor no. 1 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 1 peripheral blood monocytes, biological replicate 3, with 10 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: peripheral blood monocytes / pro-B cells

value: donor no. 1 / 129S1/SvImJ x Cast/EiJ F1


title: W1_repl2

description:
C.elegans strains (N2:Hawaii) RNA mix, library preparation replicate 2
LOVSON_E1.Roundworm_only.counts.tsv

source_name: N2 and Hawaii strains

extract_protocol:
Trizol
NEBNext® Single Cell/Low Input RNA

value: N2 and Hawaii strains


title: Dual perturb-seq screen, unstimulated, replicate 2, channel 2, mRNA

description:
10x Genomics 3' v3 mRNA library, single index
BUT290A27_BUT290A28_matrix.mtx.gz
BUT290A27_BUT290A28_barcodes.tsv.gz
BUT290A27_BUT290A28_features.tsv.gz

value: mRNA


title: donor1_biorepl2_spikein_25pRNA_W1

description:
donor no. 1 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 1 peripheral blood monocytes, biological replicate 2, with 25 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: WT


title: donor2_biorepl1_spikein_50pRNA_W1

description:
donor no. 2 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 2 peripheral blood monocytes, biological replicate 1, with 50 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: donor no. 2 / N2 x Hawaii


title: donor3_biorepl1_spikein_50pRNA_W1

description:
donor no. 3 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 3 peripheral blood monocytes, biological replicate 1, with 50 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: donor no. 3 / N2 x Hawaii


title: A549-NT(1)-rep1-vhcl [GR_1]

extract_protocol:
Chromatin immunoprecipitation followed by sequencing (ChIP)-seq was performed as previously described (Schmidt, D. et al. Methods 48, 240–248 (2009).In brief, cells were fixed in 1% formaldehyde for 10 min and quenched with 0.125M glycine. Nuclear lysates were extracted as previously described and sonicated for 13 cycles (30 sec on/30 sec off) using the Bioruptor® Pico (B01060001, Diagenode). ). Per ChIP, 50 µL of magnetic Protein A beads (10008D, Thermo Fisher Sci-entific) beads were conjugated to 7.5µL of GR antibody, or 5µg of RAD21, PAXIP1, and H3K4me1 antibodies.
Immunoprecipitated DNA was processed for library preparation usin KAPA library preparation kit, KK8234, Roche.

value: Lung Cancer

value: DMSO

value: GR (12041, Cell Signaling Technology)


title: W1_repl3

description:
C.elegans strains (N2:Hawaii) RNA mix, library preparation replicate 3
LOVSON_E1.Roundworm_only.counts.tsv

value: whole organism

value: N2 x Hawaii


title: donor3_biorepl1_spikein_25pRNA_W1

description:
donor no. 3 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 3 peripheral blood monocytes, biological replicate 1, with 25 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv


title: W1_repl1

description:
C.elegans strains (N2:Hawaii) RNA mix, library preparation replicate 1
LOVSON_E1.Roundworm_only.counts.tsv


title: donor3_biorepl1_spikein_10pRNA_M

description:
donor no. 3 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 3 peripheral blood monocytes, biological replicate 1, with 10 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: donor no. 3 / 129S1/SvImJ x Cast/EiJ F1


title: donor1_biorepl1_spikein_25pRNA_W1

description:
donor no. 1 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 1 peripheral blood monocytes, biological replicate 1, with 25 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: peripheral blood monocytes / whole organism

value: donor no. 1 / N2 x Hawaii


title: Dual perturb-seq screen, unstimulated, replicate 2, channel 1, mRNA

description:
10x Genomics 3' v3 mRNA library, single index
BUT290A25_BUT290A26_matrix.mtx.gz
BUT290A25_BUT290A26_barcodes.tsv.gz
BUT290A25_BUT290A26_features.tsv.gz

value: Human foreskin fibroblast (HFF)

value: Infected with Toxoplasma gondii RH CRISPR mutants for 24 h

value: Unstimulated


title: donor1_biorepl1_spikein_10pRNA_M

description:
donor no. 1 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 1 peripheral blood monocytes, biological replicate 1, with 10 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: peripheral blood monocytes / pro-B cells

value: donor no. 1 / 129S1/SvImJ x Cast/EiJ F1


title: Dual perturb-seq screen, unstimulated, replicate 1, channel 2, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, single index
BUT290A23_BUT290A24_matrix.mtx.gz
BUT290A23_BUT290A24_barcodes.tsv.gz
BUT290A23_BUT290A24_features.tsv.gz

value: CRISPR sgRNA


title: donor2_biorepl1_spikein_25pRNA_W1

description:
donor no. 2 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 2 peripheral blood monocytes, biological replicate 1, with 25 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: WT


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 2, RNA-seq

city: Tsu-shi

first: Rawin

last: Poonperm

state: Mie

address: 1577 Kurimamachiya

department: Graduate School of Bioresources

institute: Mie University

description:
mm9
non-haplotype resolved; excluding chrX

data_processing:
The adapter-sequence trimming and removal of low-quality base reads were performed by trim_galore version 0.6.6 (--quality 20 --phred33 --length 35)
Trimmed fastq files were aligned to the mouse genome (UCSC mm9) by tophat2 version 2.1.1.
We removed rRNA reads from the mapped reads and excluded reads from the X chromosome for genome-wide non-haplotype resolved analysis.
Filtered mapped reads were quantified against the annotated UCSC transcriptome for mm9 to calculate FPKM (Fragments per kilobase per million mapped fragments) values using the Cuffdiff program of the Cufflinks. (version 2.2.1)
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: embryonic stem cell

growth_protocol: JB4/EI7HZ2 mESCs were grown in serum containing medium + 2i/LIF [MEK and GSK3 inhibitors (2i) and leukemia inhibitory factor (LIF)] (DMEM (Nacalai , 08458-45 500 ml, or sigma, cat#D6429-500ML); 15% FBS (gibco 10270-106, lot# 42Q6272K); 1× Pen/strep (Nacalai, 09367-34); 1× Non-essential amino acid (Nacalai, 06344-56); 0.1 mM β-mercaptoethanol (Gibco, 21985-023); 1000 U/ml LIF (Nacalai USA, NU0012-2); 1 µM PD0325901 (Wako, 162-25291); 3 µM CHIR99021 (Wako, 034-23103)) on culture plate coated with 0.2% gelatin. Medium also contained 0.2 mg/ml G418 (invivogen, ant-gn-1) and 25 µg/mL Zeocin (invivogen, ant-zn-1) in order to maintain two X chromosomes state. Wild-type and SmcHD1-mutant JB4/EI7HZ2 mESCs were differentiated to neuroectoderm for 7 or 9 days as described (Miura et al., 2019). Neural stem cells (NSCs) were derived from wild-type and SmcHD1-mutant JB4/EI7HZ2 mESCs and cultured as described (Pollard et al., 2006). NSCs were cultured in NSC maintenance media [(DMEM/F12 (nacalai tesque, #11581-15); 1× N2 supplement (Thermo Fisher, 17502048); 2 mM L-Glutamine (Nacalai tesque, #16948-08); 1× Pen/strep (Nacalai tesque, 09367-34); 75 µg/ml BSA (sigma, A3311-10G); 25 µg/ml Insulin (sigma, I1882-100MG); 10 ng/ml FGF2 (Peprotech 100-18B); 10 ng/ml EGF (Funakoshi, 2028-EG-200)] on 0.2% gelatin coated plate.

extract_protocol:
RNA was harvested using Direct-zol RNA miniprep (ZymoResearch, R2050). 300 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep, Ligation (96 Samples) (Illumina, 20040534) following manufacturer's protocols.

value: embryonic stem cell

value: neural stem cells (NSCs)

value: SmcHD1 knockout

tag: Sex

value: female

value: differentiation to neural stem cells


title: Dual perturb-seq screen, interferon-gamma stimulated, replicate 1, channel 1, mRNA

description:
10x Genomics 3' v3 mRNA library, dual index
BUT290A29_BUT290A30_matrix.mtx.gz
BUT290A29_BUT290A30_barcodes.tsv.gz
BUT290A29_BUT290A30_features.tsv.gz

value: Interferon-gamma stimulated

value: mRNA


title: donor2_biorepl1_spikein_10pRNA_M

description:
donor no. 2 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 2 peripheral blood monocytes, biological replicate 1, with 10 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

tag: cell type

value: donor no. 2 / 129S1/SvImJ x Cast/EiJ F1


title: Dual perturb-seq screen, unstimulated, replicate 1, channel 2, mRNA

description:
10x Genomics 3' v3 mRNA library, single index
BUT290A23_BUT290A24_matrix.mtx.gz
BUT290A23_BUT290A24_barcodes.tsv.gz
BUT290A23_BUT290A24_features.tsv.gz


title: donor7_biorepl2_spikein_10pRNA_W1

description:
donor no. 7 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 7 peripheral blood monocytes, biological replicate 2, with 10 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: peripheral blood monocytes / whole organism

value: donor no. 7 / N2 x Hawaii


title: donor6_biorepl2_spikein_10pRNA_W1

description:
donor no. 6 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 6 peripheral blood monocytes, biological replicate 2, with 10 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: donor no. 6 / N2 x Hawaii


title: WT JB4/EI7HZ2 NSCs Replicate 3, RNA-seq


title: H1M1_94vs6_pRNA_repl3

description:
Mix of GM12878.DF1 cell line and Abl. 1 cell line (129S1xCAST F1) RNA, 94:06 proportion, library preparation replicate 3
LOVSON_E1.Human_Mouse.counts.tsv

source_name: clonal pro-B cell line GM12878.DF1 / v-Abl pro-B clonal cell line Abl.1

extract_protocol:
Agilent Mini / Agilent Mini
NEBNext® Single Cell/Low Input RNA

value: pro-B cells / pro-B cells

value: GM12878.DF1 / 129S1/SvImJ x Cast/EiJ F1


title: H1M1_94vs6_pRNA_repl2

description:
Mix of GM12878.DF1 cell line and Abl. 1 cell line (129S1xCAST F1) RNA, 94:06 proportion, library preparation replicate 2
LOVSON_E1.Human_Mouse.counts.tsv

value: clonal pro-B cell line GM12878.DF1 / v-Abl pro-B clonal cell line Abl.1


title: H1M1_94vs6_pRNA_repl1

description:
Mix of GM12878.DF1 cell line and Abl. 1 cell line (129S1xCAST F1) RNA, 94:06 proportion, library preparation replicate 1
LOVSON_E1.Human_Mouse.counts.tsv


title: donor4_biorepl2_spikein_10pRNA_W1

description:
donor no. 4 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 4 peripheral blood monocytes, biological replicate 2, with 10 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: donor no. 4 / N2 x Hawaii


title: Pilot experiment, 24 sgRNAs, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, single index
BUT290A19_BUT290A20_matrix.mtx.gz
BUT290A19_BUT290A20_barcodes.tsv.gz
BUT290A19_BUT290A20_features.tsv.gz

value: Human foreskin fibroblast (HFF)

value: Infected with Toxoplasma gondii RH CRISPR mutants for 24 h

value: Unstimulated

value: CRISPR sgRNA


title: WT JB4/EI7HZ2 NSCs Replicate 2, RNA-seq

value: embryonic stem cell

value: neural stem cells (NSCs)

value: WT


title: Dual perturb-seq screen, unstimulated, replicate 1, channel 1, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, single index
BUT290A21_BUT290A22_matrix.mtx.gz
BUT290A21_BUT290A22_barcodes.tsv.gz
BUT290A21_BUT290A22_features.tsv.gz


title: WT JB4/EI7HZ2 NSCs Replicate 1, RNA-seq

value: female

value: differentiation to neural stem cells


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 3, RNA-seq

value: SmcHD1 knockout


title: Pilot experiment, 24 sgRNAs, mRNA

description:
10x Genomics 3' v3 mRNA library, single index
BUT290A19_BUT290A20_matrix.mtx.gz
BUT290A19_BUT290A20_barcodes.tsv.gz
BUT290A19_BUT290A20_features.tsv.gz

value: mRNA


title: Dual perturb-seq screen, unstimulated, replicate 2, channel 1, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, single index
BUT290A25_BUT290A26_matrix.mtx.gz
BUT290A25_BUT290A26_barcodes.tsv.gz
BUT290A25_BUT290A26_features.tsv.gz


title: donor7_biorepl1_spikein_10pRNA_W1

description:
donor no. 7 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 7 peripheral blood monocytes, biological replicate 1, with 10 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: peripheral blood monocytes / whole organism

value: donor no. 7 / N2 x Hawaii


title: donor1_biorepl2_spikein_10pRNA_M

description:
donor no. 1 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 1 peripheral blood monocytes, biological replicate 2, with 10 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv

value: peripheral blood monocytes / pro-B cells

value: donor no. 1 / 129S1/SvImJ x Cast/EiJ F1


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 3, RNA-seq

value: day-9 differentiated ESCs

value: differentiation to embryoid body


title: H1M1_84vs16_pRNA_repl2

description:
Mix of GM12878.DF1 cell line and Abl. 1 cell line (129S1xCAST F1) RNA, 84:16 proportion, library preparation replicate 2
LOVSON_E1.Human_Mouse.counts.tsv

value: clonal pro-B cell line GM12878.DF1 / v-Abl pro-B clonal cell line Abl.1

value: pro-B cells / pro-B cells

value: GM12878.DF1 / 129S1/SvImJ x Cast/EiJ F1


title: SmcHD1-KO JB4/EI7HZ2 NSCs Replicate 1, RNA-seq

description:
mm9
non-haplotype resolved; excluding chrX


title: H1M1_84vs16_pRNA_repl3

description:
Mix of GM12878.DF1 cell line and Abl. 1 cell line (129S1xCAST F1) RNA, 84:16 proportion, library preparation replicate 3
LOVSON_E1.Human_Mouse.counts.tsv


title: H1M1_84vs16_pRNA_repl1

description:
Mix of GM12878.DF1 cell line and Abl. 1 cell line (129S1xCAST F1) RNA, 84:16 proportion, library preparation replicate 1
LOVSON_E1.Human_Mouse.counts.tsv


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 2, RNA-seq


title: Pilot experiment, 2 sgRNAs, mRNA

description:
10x Genomics 3' v3 mRNA library, single index
BUT290A1_BUT290A2_matrix.mtx.gz
BUT290A1_BUT290A2_barcodes.tsv.gz
BUT290A1_BUT290A2_features.tsv.gz

value: Human foreskin fibroblast (HFF)

value: Infected with Toxoplasma gondii RH CRISPR mutants for 24 h

value: Unstimulated


title: donor5_biorepl1_spikein_10pRNA_W1

description:
donor no. 5 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 5 peripheral blood monocytes, biological replicate 1, with 10 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: WT

value: donor no. 5 / N2 x Hawaii


title: mouse3_liver_chunk1_repl2_spikeinW3

description:
Mouse no.3 (129S1xCAST F1), liver, with C.elegans (1:2 N2:Hawaii) RNA spike-in, library preparation replicate 2
POLMOT_E2.Mouse_Roundworm.counts.tsv

organism:
Caenorhabditis elegans
Mus musculus

source_name: liver / whole organism

value: liver / whole organism

value: 129S1/SvImJ x Cast/EiJ F1 / N2 x Hawaii


title: Dual perturb-seq screen, unstimulated, replicate 1, channel 1, mRNA

description:
10x Genomics 3' v3 mRNA library, single index
BUT290A21_BUT290A22_matrix.mtx.gz
BUT290A21_BUT290A22_barcodes.tsv.gz
BUT290A21_BUT290A22_features.tsv.gz

value: mRNA


title: donor5_biorepl2_spikein_10pRNA_W1

description:
donor no. 5 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 5 peripheral blood monocytes, biological replicate 2, with 10 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: peripheral blood monocytes / whole organism


title: donor4_biorepl1_spikein_10pRNA_W1

description:
donor no. 4 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 4 peripheral blood monocytes, biological replicate 1, with 10 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: donor no. 4 / N2 x Hawaii


title: mouse3_liver_chunk1_repl1_spikeinW1

description:
Mouse no.3 (129S1xCAST F1), liver, with C.elegans (1:1 N2:Hawaii) RNA spike-in, library preparation replicate 1
POLMOT_E2.Mouse_Roundworm.counts.tsv


title: Healthy control (Group 4, C11)

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

country: Italy

institute: University of Padova

description: miRNA expression profiling of healthy control (Group 4, C11)

hyb_protocol: Probes were hybridized at 55°C for 22 hours using the Agilent's hybridization oven that is suited for bubble-mixing and microarray hybridization processes.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 10% sensitivity settings. Agilent Feature Extraction software version 12.0.0.7 was used for image analysis.

data_processing: Inter-array normalization of miRNA expression levels was performed with cyclic Lowess for miR [Risso et al., 2009] and the average of replicates was used. Feature Extraction software (Agilent Technologies) was used to obtain spot quality measures in order to evaluate the quality and the reliability of the hybridization. In particular, the flag “glsFound” (set to 1 if the spot has an intensity value significantly different from the local background, 0 otherwise) was used to filter out unreliable probes: flag equal to 0 will be noted as “not available” (NA). So, in order to perform a more robust and unbiased statistical analysis, probes with a high proportion of NA values were removed from the dataset. NA (44%) was used as threshold in the filtering process, obtaining a total of 210 available human miRNAs.

source_name: Olfactory epithelium cells (OE)

label_protocol: Total RNA (200 ng) was labeled with pCp Cy3, according to the Agilent’s protocol, and unincorporated dyes were removed with MicroBioSpin6 columns (BioRad, Hercules, CA, USA)

extract_protocol: Total RNA, including miRNAs, was extracted from the olfactory epithelium cells by using “Monarch® Total RNA Miniprep kit” (New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s instructions. Briefly, this kit is a comprehensive solution for sample preservation, cell lysis, gDNA removal, and purification of total RNA from a wide variety of biological samples, including mammalian tissue. Total RNA was quantified by Nanodrop (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity, and the content of miRNAs (%) in each sample were assessed by capillary electrophoresis with the RNA 6000 Nano LabChip and the Small RNA Nano LabChip, respectively, using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Only samples with RNA Integrity Number (R.I.N.) values higher than six were used for gene and miRNA expression analysis.

value: olfactory epithelium


title: donor1_biorepl3_spikein_10pRNA_W1

description:
donor no. 1 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 1 peripheral blood monocytes, biological replicate 3, with 10 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: donor no. 1 / N2 x Hawaii


title: mouse2_liver_chunk1_repl2_spikeinW2

description:
Mouse no.2 (129S1xCAST F1), liver, with C.elegans (2:1 N2:Hawaii) RNA spike-in, library preparation replicate 2
POLMOT_E2.Mouse_Roundworm.counts.tsv


title: donor1_biorepl2_spikein_10pRNA_W1

description:
donor no. 1 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 1 peripheral blood monocytes, biological replicate 2, with 10 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv


title: Healthy control (Group 4, C10)

description: miRNA expression profiling of healthy control (Group 4, C10)


title: donor3_biorepl1_spikein_10pRNA_W1

description:
donor no. 3 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 3 peripheral blood monocytes, biological replicate 1, with 10 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: donor no. 3 / N2 x Hawaii