title: Donor1 G472 RNP only - [CD5-NGS-revision-VVPlate-2A02_S105]


title: BL6_iBAT_hfd_cold_2

status: Public on May 12 2022

type: SRA

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

library_source: transcriptomic

data_processing:
barcode and adapter removal using flexbar 3.4.0
quality trimming using cutadapt
quantification of transcripts (combination of GENCODE M22 and RNAcentral 5) by salmon
normalisation and differential gene expression analysis using DESeq2
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: iBAT

extract_protocol:
All tissues were dissected, washed with PBS and weighed. They were snap-frozen in liquid nitrogen and stored at -80C. Total RNA was isolated using peqGOLD TriFast (PEQLAB Biotechnologie).
genomic DNA was eliminated following the instructions of the TURBO DNA-freeTM Kit. Total RNA libraries were constructed using the Illumina TruSeq kit following the manufacturer's protocol.

treatment_protocol: Wild type C57BL/6N mice were fed chow diet (Ssniff V1554) up to the age of 8 weeks, where the respective cohorts were put on HFD (Ssniff D12492 (I) mod.) for 12 weeks and kept at 4◦ C for 24 h.

tag: strain

tag: tissue

value: iBAT

tag: diet

value: hfd

tag: treatment

value: cold

tag: batch


title: BL6_iBAT_hfd_rt_1

value: rt


title: Patient37

type: RNA

city: New York

first: Department of Pathology

last: NYU Langone Health

state: NY

address: 240 East 38th Street

department: Department of Pathology

country: USA

institute: NYU Langone Health Ambulatory Care Center

description:
15-180
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

hyb_protocol: Quality metrics for extracted RNA included both quantitative and qualitative parameters. RNA quantification was performed with the Qubit 2.0 Fluorometer (Life Technologies).

scan_protocol: Qualitative RNA integrity was performed with the Agilent 2100 Bioanalyzer System (Agilent software, Santa Clara, CA, USA) and corresponding RNA kits. Electropherograms showing fragment distribution were reviewed; only cases with an RNA integrity number of >3 were selected.

data_processing: RCC files for tumor samples are direct outputs from NanoString runs. We then extract raw counts for each gene in a sample in R.

organism: Homo sapiens

source_name: Melanoma

extract_protocol:
Tumor samples were dissected and de-paraffinized using the same methods described in the DNA analysis.
RNA was isolated using the Qiagen RNeasy DSP FFPE Kit, and melanotic samples were purified as the DNA samples were.

value: Melanoma

tag: nf1 status

value: MUT


title: Patient41

description:
04-127
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: DSP-1001660003683-G-E07

city: Cambridge

first: Karthik

last: Jagadeesh

state: MA

address: 415 Main St

department: Human Cell Atlas

institute: Broad Institute

data_processing:
Library strategy: NanoString whole-transcriptome digital spatial profiling
Process FASTQ sequencing files (from Illumina NGS run) to DCC digital count files using Nanostring GeoMx NGS Pipeline v1.0
Generate raw and normalized count matrices using Nanostring azorius and hydra scripts, as described in associated manuscript
Assembly: Nanostring GeoMx human whole transcriptome atlas; found in geomx_ngs_data_second_acquisition_WTA_Hs_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: Txt file of uncollapsed raw counts matrix; found in hPDAC_WTA_20210222T2101_TargetCountMatrix.txt
Supplementary files format and content: Txt file of bioprobe QC counts matrix; found in hPDAC_WTA_20210222T2101_BioProbeCountMatrix.txt
Supplementary files format and content: Txt file of negative probe normalized counts matrix; found in hPDAC_WTA_20210222T2101_NegNorm_TargetCountMatrix.txt
Supplementary files format and content: Txt file of q3 normalized counts matrix; found in hPDAC_WTA_20210222T2101_Q3Norm_TargetCountMatrix.txt

source_name: Pancreas

extract_protocol:
In brief, we sectioned clinical FFPE blocks at 5 um onto SuperFrost Plus microscopy slides and then followed the manufacturer instructions for RNA (NanoString) with minor modifications as noted in the associated manuscript.
Libraries were constructed according to manufacturer protocols (NanoString) for sequencing on a NovoSeq S2 (Illumina) with the following paired end read configuration: read 1, 27 nt; read 2, 27 nt; index 1, 8 nt; index 2, 8 nt.

treatment_protocol: 14 specimens received no treatment prior to resection; 7 specimens received neoadjuvant chemotherapy, radiotherapy, losartan, and/or nivolumab prior to resection

value: Pancreas

tag: treatment / other annotation

value: Untreated


title: Patient36

description:
15-130
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: WT


title: BL6_iBAT_ncd_rt_2

value: ncd


title: Patient35

description:
15-079
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: BL6_iBAT_ncd_rt_1


title: DSP-1001660003683-G-F11


title: Patient42

description:
07-120
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Patient34

description:
15-018
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: BL6_iBAT_hfd_rt_2


title: Donor2 G472 CD5-HA dsDNA 4 pmol [CD5-NGS-revision-VVPlate-1F09_S70]

city: San Francisco

first: Vivasvan

last: Vykunta

state: CA

address: 513 Parnassus Avenue HSW901

institute: Gladstone-UCSF Institute of Genomic Immunology

library_source: genomic

data_processing:
library strategy: amplicon sequencing
Data was processed to calculate insertions/deletions at the CD5 target site with Crispresso2 version 2.2.7 (Clement et al., 2019) with the following options "--skip_failed", "--default_min_aln_score 60", "--min_average_read_quality 30", " --exclude_bp_from_left 40", " --exclude_bp_from_right 40", "--annotate_wildtype_allele CD5_WT", " --min_frequency_alleles_around_cut_to_plot 0.05", "--expected_hdr_amplicon_seq GGAGAAGGGAGAGAGTGGGAGGTTTCACTTCCTGACCCTCCTCTCTTCTTTCTGCAGTCGCTTCCTGCCTCGGAtacccatacgatgtgcctgattacgcaggatcaCGGCTCAGCTGGTATGACCCAGGTAAGGAAGAGCCACATGGAGAAAGGCCTGGGGCAGGGGGAGAGTGGGGCTGTGGTTTCATCAGGCCATCG", " --coding_seq GCTTCCTGCCTCGGACGGCTCAGCTGGTATGACCCA", and " --ignore_substitutions".
Assembly: hg38

molecule: genomic DNA

source_name: primary Bulk T human cells

growth_protocol: Cells were activated at 1e6  cells per mL  for 2 days in complete XVivo15 medium (Lonza) (5% fetal bovine serum, 50 µM 2-mercaptoethanol, 10 mM N-acetyl L-cysteine) supplemented with anti-human CD3/CD28 magnetic Dynabeads (CTS, ThermoFisher) in a 1:1 ratio with cells, 500 U mL-1  of IL-2 (UCSF Pharmacy), and 5 ng mL-1  of IL-7 and IL-15 (R&D Systems).

extract_protocol:
5 days after electroporations, genomic DNA was isolated from each sample using DNA QuickExtract (Lucigen, Cat#QE09050) based on manufacturer protocols.
Primers were designed around the guideRNA target site and included adapter sequences. Amplicons were generated by adding 0.5 µL each of forward and reverse primer at 100 µM to 10 µL of QuickExtract, 50 µL of KAPA HiFi HotStart Ready Mix PCR kit (Roche, Cat# 07958935001), and H2O to a total of 100 uL reaction volume. The following PCR thermocycler conditions were followed: 95°C for 3 minutes, 30 cycles of 98°C for 30 seconds followed by 68°C for 30 seconds and 72°C for 30 seconds, and a final 3 minute extension at 72°C. Amplicons were submitted to the Innovative Genomics Institute (IGI) Next Generation Sequencing Core for second PCR reactions and sequencing.

treatment_protocol: GuideRNA/Cas9 ribonucleoprotein complexes (50 pmols unless stated otherwise) targeting CD5 were electroporated into primary Bulk T human cells with indicated dose of a homology directed repair template.

tag: cell type

value: primary Bulk T human cells

value: G472 CD5-HA dsDNA 4 pmol


title: DSP-1001660003683-G-E03


title: Donor2 G472 CD5-HA dsDNA CTS 4 pmol [CD5-NGS-revision-VVPlate-1F10_S78]

value: G472 CD5-HA dsDNA CTS 4 pmol


title: DSP-1001660003683-G-F08


title: CTO19 7d noEGF replica1

city: Barcelona

first: Adria

last: Caballe

address: C/ Baldiri Reixac 10

department: biostatistics

country: Spain

institute: IRB

data_processing:
Alignment software: STAR version 2.7.0a with default parameters and annotated genome with GENCODE mouse release M25
Sam to BAM and sorting: sambamba version 0.5.9
Read counts: Rsubread version 2.4.3 with GENCODE M25 annotation and default parameters
Genome_build: mm10
Supplementary_files_format_and_content: Expression matrix of raw counts

source_name: APS colon cancer organoids

growth_protocol: Organoids were grown in media with B27, noggin, Galunisertib and EGF for 3 days prior to extraction for the control media conditions. EGF was removed from the media from d0, and organoids were grown for 7 days in the no EGF condition

extract_protocol:
RNA was extracted following the indications of PURELINK RNA MINI KIT (Thermofisher)
RNA libraries were prepared for sequencing using the kits NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# E7490) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (Cat#E7770), following manufacturer´s instructions and 8 cycles of amplification.

value: APS colon cancer organoids

tag: sample id

tag: sample barcode

value: GGCTAC

tag: gender

value: Male

tag: media

value: noEGF media

tag: time

tag: condition

tag: replicate


title: Donor2 G472 RNP only - [CD5-NGS-revision-VVPlate-1F08_S62]

value: G472 RNP only -


title: CTO19 7d noEGF replica2

value: CTTGTA


title: DSP-1001660003683-G-F05


title: Patient32

description:
14-201
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Patient33

description:
15-009
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: DSP-1001660003683-G-F06


title: DSP-1001660003683-G-F04


title: Donor2 G472 CD5-HA ssDNA CTS 4 pmol [CD5-NGS-revision-VVPlate-1F12_S94]

value: G472 CD5-HA ssDNA CTS 4 pmol


title: CTO19 3d EM replica2

value: GATCAG

value: Control media (EM)


title: DSP-1001660003683-G-E01


title: Donor2 no electro No HDRT - [CD5-NGS-revision-VVPlate-1F07_S54]

value: no electro No HDRT -


title: Donor2 G472 CD5-HA ssDNA 4 pmol [CD5-NGS-revision-VVPlate-1F11_S86]

value: G472 CD5-HA ssDNA 4 pmol


title: Donor1 G472 CD5-HA ssDNA 4 pmol [CD5-NGS-revision-VVPlate-1F05_S38]


title: Patient30

description:
13-215
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: Melanoma

value: MUT


title: CTO19 3d EM replica1

value: CAGATC


title: apsMC706 7d noEGF replica2

value: GCCAAT

value: Female


title: Patient29

description:
13-191
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: WT


title: Patient31

description:
14-129
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Donor1 G472 CD5-HA ssDNA CTS 4 pmol [CD5-NGS-revision-VVPlate-1F06_S46]

value: primary Bulk T human cells


title: Donor1 G472 CD5-HA dsDNA CTS 4 pmol [CD5-NGS-revision-VVPlate-1F04_S30]

value: G472 CD5-HA dsDNA CTS 4 pmol


title: apsMC706 3d EM replica2

value: APS colon cancer organoids

value: TGACCA


title: apsMC706 7d noEGF replica1

value: ACAGTG

value: noEGF media


title: Patient28

description:
13-137
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: DSP-1001660003683-G-E06

value: Pancreas

value: Untreated


title: Patient27

description:
13-045
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Donor1 G472 RNP only - [CD5-NGS-revision-VVPlate-1F02_S14]

value: G472 RNP only -


title: DSP-1001660003683-G-D10


title: DSP-1001660003683-G-E10


title: DSP-1001660003683-G-F01


title: Donor1 G472 CD5-HA dsDNA 4 pmol [CD5-NGS-revision-VVPlate-1F03_S22]

value: G472 CD5-HA dsDNA 4 pmol


title: MTO101 p9 +6 d4 pool 2

data_processing:
Alignment software: STAR version 2.3.0e with default parameters and annotated genome mm10
Sam to BAM and sorting: sambamba version 0.6.7
Read counts: Rsubread version 1.32.4 with Ensembl annotation mm10 and default parameters
Count normalization: DESeq2 version 1.22.1 function "counts" with normalization parameter=TRUE
Genome_build: mm10
Supplementary_files_format_and_content: Expression matrix of raw counts with the DESeq2 function "counts" and normalization parameter = TRUE

source_name: MTO101 p9 +6 d4 pool 2

growth_protocol: MTOs were cultured at 37 °C with 85–90% humidity, atmospheric O2 and 5% CO2. For MTO passaging, basement-membrane extract drops were washed once with HBSS (Lonza) and treated with Trypsin-EDTA (Sigma) for 20 min at 37 °C, followed by mechanical disaggregation of organoid fragments (by pipetting) until a single-cell suspension was obtained. Trypsin was quenched with FBS, cells were washed with HBSS and replated in cold BME medium on warm plates.

extract_protocol:
Organoids were lyzed with Trizol and RNA was purified using PureLink® RNA Mini Kit
RNA libraries were prepared for sequencing using the kits NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# E7490) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (Cat#E7770), following manufacturer´s instructions and 9-10 cycles of amplification.

treatment_protocol: Organoids were cultured with tumour organoid culture medium (see Tauriello et al. 2018; advanced DMEM/F12, supplemented with 10 mM HEPES,Glutamax, B-27 without retinoic acid (all Life Technologies), 50 ng/ml recombinant human EGF (Peprotech), 100 ng/ml recombinant human NOGGIN and 1 μ M galunisertib (LY2157299). We used 3 conditions: full medium, medium without EGF and medium without galunisertib but with TGFβ1 (5 ng/ul).

value: AGTCAA

tag: genotype

value: triple

tag: interv

value: krasWT

tag: medium

value: full

tag: mto

tag: pool


title: DSP-1001660003683-G-E05

tag: tissue


title: MTO101 p9 no EGF d7 pool 2

source_name: MTO101 p9 no EGF d7 pool 2

value: AGTTCC

value: noEGF


title: Patient26

description:
12-210
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: Melanoma

value: WT


title: Patient25

description:
12-203
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Donor1 no electro No HDRT - [CD5-NGS-revision-VVPlate-1F01_S6]

value: primary Bulk T human cells

tag: treatment

value: no electro No HDRT -


title: Patient24

description:
12-110
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

tag: nf1 status


title: Donor2 G472 CD5-HA ssDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-1E12_S93]

value: G472 CD5-HA ssDNA CTS 20 pmol


title: Donor2 G472 CD5-HA ssDNA 20 pmol [CD5-NGS-revision-VVPlate-1E11_S85]

value: G472 CD5-HA ssDNA 20 pmol


title: MTO100 p11 no EGF d7 pool 2

source_name: MTO100 p11 no EGF d7 pool 2

value: CTTGTA


title: apsMC706 3d EM replica1

value: APS colon cancer organoids

value: CGATGT

tag: strain

value: Female

value: Control media (EM)


title: MTO100 p11 +6 d4 pool 2

source_name: MTO100 p11 +6 d4 pool 2

value: GGCTAC


title: DSP-1001660003683-G-E11

value: Pancreas

tag: treatment / other annotation

value: Untreated


title: Patient23

description:
12-049
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Patient22

description:
12-019
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: DSP-1001660003683-G-E04


title: Donor2 G472 CD5-HA dsDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-1E10_S77]

tag: cell type

value: G472 CD5-HA dsDNA CTS 20 pmol


title: DSP-1001660003683-G-D09


title: MTO220 p11 +6  d4 pool 2

source_name: MTO220 p11 +6  d4 pool 2

tag: sample id

tag: sample barcode

value: GATCAG

value: triple

value: full


title: MTO220 p11 TGFb d7 pool 2

source_name: MTO220 p11 TGFb d7 pool 2

value: TAGCTT

value: TGFb


title: Donor2 G472 CD5-HA dsDNA 20 pmol [CD5-NGS-revision-VVPlate-1E09_S69]

value: primary Bulk T human cells

value: G472 CD5-HA dsDNA 20 pmol


title: Patient20

description:
11-306
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: Melanoma

value: MUT


title: Donor2 G472 RNP only - [CD5-NGS-revision-VVPlate-1E08_S61]

value: G472 RNP only -


title: MTO54 p15 TGFb d7 pool 2

source_name: MTO54 p15 TGFb d7 pool 2

value: ACTTGA


title: Patient19

description:
11-285
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Patient21

description:
12-001
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: WT


title: Donor2 no electro No HDRT - [CD5-NGS-revision-VVPlate-1E07_S53]

value: no electro No HDRT -


title: DSP-1001660003683-G-D11


title: DSP-1001660003683-G-D03


title: MTO101 p8 no EGF d7 pool 1

source_name: MTO101 p8 no EGF d7 pool 1

value: GTCCGC

value: krasWT

value: noEGF


title: Donor1 G472 CD5-HA ssDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-1E06_S45]

value: G472 CD5-HA ssDNA CTS 20 pmol


title: DSP-1001660003683-G-D12

value: Pancreas

value: Untreated


title: Patient18

description:
11-258
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Donor1 G472 CD5-HA ssDNA 20 pmol [CD5-NGS-revision-VVPlate-1E05_S37]

value: G472 CD5-HA ssDNA 20 pmol


title: MTO54 p15 +6 d4 pool 2

source_name: MTO54 p15 +6 d4 pool 2

value: CAGATC

value: triple

value: full


title: DSP-1001660003683-G-D06


title: DSP-1001660003683-G-D08


title: DSP-1001660003683-G-A10


title: MTO101 p8 +6 d4 pool 1

source_name: MTO101 p8 +6 d4 pool 1

value: CCGTCC


title: Patient17

description:
11-047
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: Melanoma


title: Donor1 G472 CD5-HA dsDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-1E04_S29]

value: primary Bulk T human cells

value: G472 CD5-HA dsDNA CTS 20 pmol


title: DSP-1001660003683-G-E02


title: Patient15

description:
10-286
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: MUT


title: MTO100 p10 no EGF d7 pool 1

source_name: MTO100 p10 no EGF d7 pool 1

value: ATGTCA


title: MTO100 p10 +6 d4 pool 1

source_name: MTO100 p10 +6 d4 pool 1

value: AGTTCC


title: Patient16

description:
10-298
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Donor1 G472 CD5-HA dsDNA 20 pmol [CD5-NGS-revision-VVPlate-1E03_S21]

value: G472 CD5-HA dsDNA 20 pmol


title: Donor1 no electro No HDRT - [CD5-NGS-revision-VVPlate-1E01_S5]

value: no electro No HDRT -


title: DSP-1001660003683-G-D01


title: Donor1 G472 RNP only - [CD5-NGS-revision-VVPlate-1E02_S13]

value: G472 RNP only -


title: DSP-1001660003683-G-C02


title: Patient12

description:
10-108
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: MTO54 p14 TGFb d7 pool 1

source_name: MTO54 p14 TGFb d7 pool 1

value: GGCTAC

value: TGFb


title: Patient11

description:
07-017
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

source_name: Melanoma

value: WT


title: DSP-1001660003683-G-C07

source_name: Pancreas

value: Pancreas

value: Untreated


title: DSP-1001660003683-G-D02


title: DSP-1001660003683-G-D07


title: Patient13

description:
10-187
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Donor2 G472 CD5-HA dsDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-1D10_S76]

source_name: primary Bulk T human cells

value: G472 CD5-HA dsDNA CTS 100 pmol


title: DSP-1001660003683-G-C10


title: Donor2 G472 CD5-HA ssDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-1D12_S92]

value: G472 CD5-HA ssDNA CTS 100 pmol


title: Donor2 G472 CD5-HA dsDNA 100 pmol [CD5-NGS-revision-VVPlate-1D09_S68]

value: G472 CD5-HA dsDNA 100 pmol


title: aos wounded petiole sample under low R/FR from A. thaliana after 4h [2.3]

city: Lausanne

first: Emanuel

last: Schmid-Siegert

address: UNIL Sorge

country: Switzerland

institute: UNIL

description:
ASF_16C
PolyA
aos.low.wound.2.3
processed data file: genes.counts.normalized.txt

data_processing:
Trimming with trim_galore 0.4.4 “-q 30 --length 40”
Mapping with STAR 2.5.0 “-- outFilterMismatchNmax 4”
Gene count with STAR 2.5.0.
Filtering low expression with average logCPM < -0.5.
Differential expression analysis with EdgeR 3.18.1 and Limma 3.32.5.
Genome_build: TAIR10.29
Supplementary_files_format_and_content: genes.counts.normalized.txt: Tab-delimited text file includes normalized log2 CPM values.

organism: Arabidopsis thaliana

source_name: Petiole samples

growth_protocol: Soil short days.

extract_protocol:
Petiole samples grinded in a tissue lyser, total RNA extracted using Macherey-Nagel plant RNA extraction kit. RNA was resuspended in 40uL RNase-free water and quality controlled on a Fragment Analyser.
Libraries were prepared by the Lausanne Genomic Technologies Facility from 400 ng total RNA using TruSeq stranded mRNA method.

tag: ecotype/background

tag: genotype/variation

value: aos

value: Petiole

tag: age

value: 18 days post germination

tag: light

value: low R/FR

tag: wounding

value: yes


title: MTO54 p14 +6 d4 replicate 1

source_name: MTO54 p14 +6 d4 replicate 1

value: TAGCTT

tag: genotype

value: triple

tag: interv

value: full


title: Donor2 G472 CD5-HA ssDNA 100 pmol [CD5-NGS-revision-VVPlate-1D11_S84]

value: primary Bulk T human cells

value: G472 CD5-HA ssDNA 100 pmol


title: MTO220 p10 TGFb d7 pool 1

source_name: MTO220 p10 TGFb d7 pool 1

value: AGTCAA

tag: medium

value: TGFb

tag: mto


title: aos wounded petiole sample under high R/FR from A. thaliana after 4h [2.3]

description:
ASF_14C
PolyA
aos.high.wound.2.3
processed data file: genes.counts.normalized.txt

tag: tissue

value: high R/FR

tag: time


title: Patient9

description:
08-235
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: Melanoma

tag: nf1 status

value: MUT


title: Patient8

description:
08-135
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: aos wounded petiole sample under low R/FR from A. thaliana after 1h30 [1.3]

description:
ASF_12C
PolyA
aos.low.wound.1.3
processed data file: genes.counts.normalized.txt


title: DSP-1001660003683-G-D05

value: Pancreas

value: Untreated


title: Donor2 no electro No HDRT - [CD5-NGS-revision-VVPlate-1D07_S52]

tag: treatment

value: no electro No HDRT -


title: Donor2 G472 RNP only - [CD5-NGS-revision-VVPlate-1D08_S60]

value: G472 RNP only -


title: Patient14

description:
10-280
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: aos wounded petiole sample under high R/FR from A. thaliana after 1h30 [1.3]

description:
ASF_10C
PolyA
aos.high.wound.1.3
processed data file: genes.counts.normalized.txt

value: aos

value: Petiole

value: 18 days post germination


title: Donor1 G472 CD5-HA ssDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-1D06_S44]

value: G472 CD5-HA ssDNA CTS 100 pmol


title: MTO220 p10 +6  d4 pool 1

source_name: MTO220 p10 +6  d4 pool 1

value: CTTGTA

value: triple

tag: pool


title: DSP-1001660003683-G-C12

tag: treatment / other annotation


title: DSP-1001660003683-G-D04


title: Patient7

description:
08-042
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Donor1 G472 CD5-HA dsDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-1D04_S28]

tag: cell type

value: primary Bulk T human cells

value: G472 CD5-HA dsDNA CTS 100 pmol


title: Patient5

description:
06-092
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: WT


title: aos unwounded petiole sample under low R/FR from A. thaliana after 4h [2.3]

description:
ASF_15C
PolyA
aos.low.no_wound.2.3
processed data file: genes.counts.normalized.txt

value: low R/FR

value: no


title: Patient3

description:
04-069
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: Melanoma


title: DSP-1001660003683-G-A09


title: aos unwounded petiole sample under low R/FR from A. thaliana after 1h30 [1.3]

description:
ASF_11C
PolyA
aos.low.no_wound.1.3
processed data file: genes.counts.normalized.txt


title: DSP-1001660003683-G-B11


title: Patient10

description:
09-241
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: MUT


title: Donor1 G472 CD5-HA ssDNA 100 pmol [CD5-NGS-revision-VVPlate-1D05_S36]

value: G472 CD5-HA ssDNA 100 pmol


title: aos unwounded petiole sample under high R/FR from A. thaliana after 1h30 [1.3]

description:
ASF_9C
PolyA
aos.high.no_wound.1.3
processed data file: genes.counts.normalized.txt

value: high R/FR


title: Donor1 G472 CD5-HA dsDNA 100 pmol [CD5-NGS-revision-VVPlate-1D03_S20]

value: G472 CD5-HA dsDNA 100 pmol


title: DSP-1001660003683-G-B01

value: Pancreas

value: Untreated


title: DSP-1001660003683-G-C11


title: aos unwounded petiole sample under high R/FR from A. thaliana after 4h [2.3]

description:
ASF_13C
PolyA
aos.high.no_wound.2.3
processed data file: genes.counts.normalized.txt

value: aos

value: Petiole


title: WT wounded petiole sample under low R/FR from A. thaliana after 4h [2.3]

description:
ASF_8C
PolyA
Col.low.wound.2.3
processed data file: genes.counts.normalized.txt

value: 18 days post germination

value: yes


title: DSP-1001660003683-G-B12


title: Donor1 no electro No HDRT - M [CD5-NGS-revision-VVPlate-1D01_S4]

value: no electro No HDRT - M


title: Patient6

description:
07-010
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: WT wounded petiole sample under low R/FR from A. thaliana after 1h30 [1.3]

description:
ASF_4C
PolyA
Col.low.wound.1.3
processed data file: genes.counts.normalized.txt


title: Donor2 G472 CD5-HA ssDNA CTS 4 pmol [CD5-NGS-revision-VVPlate-1C12_S91]

value: primary Bulk T human cells

value: G472 CD5-HA ssDNA CTS 4 pmol


title: DSP-1001660003683-G-A06


title: Hi-C_embryo_WT_0_rep3

first: Maria Cristina

last: Gambetta

address: Genopode Building

department: Center for Integrative Genomics

institute: University of Lausanne

description: Hi-C library

data_processing:
The FASTQ read pairs were analyzed with a Perl script to locate and separate fusion sites using the patterns /GTATAC/, /TTATAA/, /GTATAA/ and /TTATAC/.
The maximal length of each read was trimmed at 60 nucleotides, then reads were mapped to the dm6 genome using MicMap (v2.2) and matched to the genomic region (fragment) defined by the nearest upstream and downstream restriction sites.
Read pairs were discarded if they (1) mapped to non-unique positions in the reference genome, (2) had indels or >2 mismatches per read, (3) represented fusion of 2 oppositely oriented reads within 2 kb of each other, which may have not resulted from ligation of 2 digested fragments, (4) were likely additional copies of a given read pair, i.e. likely PCR duplicates.
Genome_build: dm6
Supplementary_files_format_and_content: Number of read pairs between pairs of fragments in bedpe file format (tab-delimited with columns chrom1, start1, end1, chrom2, start2, end2, number of read pairs). Supplementary file fragments.bed.gz contains a list of all possible genomic restriction fragments resulting from double digestion of genomic DNA with Csp6I and MseI enzymes in bed file format (tab-delimited with columns chromosome, start, end)

organism: Drosophila melanogaster

source_name: WT 2-6 hour old embryos, rep3

growth_protocol: standard Drosophila culture at 25°C

extract_protocol:
100 embryos were dechorionated, then homogenized in RPMI supplemented with 10% fetal bovine serum with a micropestle. Cells were crosslinked then subjected to Hi-C, cutting sequentially with MseI and Csp6I restriction enzymes.
NEBNext Ultra II DNA Library Prep kit for Illumina

treatment_protocol: Animals were not subjected to any particular treatment.

tag: strain

value: WT[0] (matched wildtype control)

value: whole embryo

value: 2-6 hour old


title: Patient2

description:
03-139
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.

value: Melanoma

value: WT


title: DSP-1001660003683-G-C08


title: Hi-C_embryo_WT_0_rep1

description: Hi-C library

source_name: WT 2-6 hour old embryos, rep1


title: Donor1 G472 RNP only - [CD5-NGS-revision-VVPlate-1D02_S12]

value: G472 RNP only -


title: DSP-1001660003683-G-C09


title: Donor2 G472 CD5-HA dsDNA 4 pmol [CD5-NGS-revision-VVPlate-1C09_S67]

value: G472 CD5-HA dsDNA 4 pmol


title: Donor2 G472 CD5-HA dsDNA CTS 4 pmol [CD5-NGS-revision-VVPlate-1C10_S75]

value: G472 CD5-HA dsDNA CTS 4 pmol


title: Hi-C_embryo_WT_0_rep2

description: Hi-C library

source_name: WT 2-6 hour old embryos, rep2


title: Donor2 G472 RNP only - [CD5-NGS-revision-VVPlate-1C08_S59]


title: Patient1

description:
03-129
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Patient4

description:
06-001
Gene expression of the nCounter PanCancer IO 360 panel for the tumor, microenvironment and immune response.


title: Donor2 G472 CD5-HA ssDNA 4 pmol [CD5-NGS-revision-VVPlate-1C11_S83]

value: G472 CD5-HA ssDNA 4 pmol


title: Hi-C_embryo_WT_0_rep4

description: Hi-C library

source_name: WT 2-6 hour old embryos, rep4


title: WT wounded petiole sample under high R/FR from A. thaliana after 1h30 [1.3]

description:
ASF_2C
PolyA
Col.high.wound.1.3
processed data file: genes.counts.normalized.txt

tag: ecotype/background

value: high R/FR


title: WT unwounded petiole sample under low R/FR from A. thaliana after 1h30 [1.3]

description:
ASF_3C
PolyA
Col.low.no_wound.1.3
processed data file: genes.counts.normalized.txt

tag: genotype/variation

value: low R/FR

value: no


title: Hi-C_embryo_CTCF_0_Cp190_0_rep2

description: Hi-C library

source_name: double[0] 2-6 hour old embryos, rep2

tag: age


title: Donor2 no electro No HDRT - [CD5-NGS-revision-VVPlate-1C07_S51]

value: no electro No HDRT -


title: WT unwounded petiole sample under low R/FR from A. thaliana after 4h [2.3]

description:
ASF_7C
PolyA
Col.low.no_wound.2.3
processed data file: genes.counts.normalized.txt

value: Petiole

value: 18 days post germination

tag: light


title: Hi-C_embryo_CTCF_0_Cp190_0_rep3

description: Hi-C library

source_name: double[0] 2-6 hour old embryos, rep3


title: Donor1 G472 CD5-HA ssDNA CTS 4 pmol [CD5-NGS-revision-VVPlate-1C06_S43]

value: primary Bulk T human cells


title: DSP-1001660003683-G-C03

value: Pancreas

value: Untreated


title: Hi-C_embryo_CTCF_0_Cp190_0_rep4

description: Hi-C library

source_name: double[0] 2-6 hour old embryos, rep4

value: whole embryo


title: DSP-1001660003683-G-C06


title: WT wounded petiole sample under high R/FR from A. thaliana after 4h [2.3]

description:
ASF_6C
PolyA
Col.high.wound.2.3
processed data file: genes.counts.normalized.txt

tag: wounding

value: yes


title: Hi-C_embryo_CTCF_0_Cp190_0_rep1

description: Hi-C library

source_name: double[0] 2-6 hour old embryos, rep1

value: 2-6 hour old

tag: genotype


title: aos wounded petiole sample under low R/FR from A. thaliana after 4h [2.2]

description:
ASF_16B
PolyA
aos.low.wound.2.2
processed data file: genes.counts.normalized.txt

value: aos


title: DSP-1001660003683-G-C04


title: DSP-1001660003683-G-A02


title: Donor1 G472 CD5-HA ssDNA 4 pmol [CD5-NGS-revision-VVPlate-1C05_S35]


title: Hi-C_embryo_CTCF_0_rep4

description: Hi-C library

source_name: CTCF[0] 2-6 hour old embryos, rep4


title: aos wounded petiole sample under low R/FR from A. thaliana after 1h30 [1.2]

description:
ASF_12B
PolyA
aos.low.wound.1.2
processed data file: genes.counts.normalized.txt


title: DSP-1001660003683-G-C05


title: aos wounded petiole sample under high R/FR from A. thaliana after 4h [2.2]

description:
ASF_14B
PolyA
aos.high.wound.2.2
processed data file: genes.counts.normalized.txt


title: WT unwounded petiole sample under high R/FR from A. thaliana after 4h [2.3]

description:
ASF_5C
PolyA
Col.high.no_wound.2.3
processed data file: genes.counts.normalized.txt

value: WT


title: Hi-C_embryo_CTCF_0_rep3

description: Hi-C library

source_name: CTCF[0] 2-6 hour old embryos, rep3


title: DSP-1001660003683-G-B07


title: Donor1 G472 CD5-HA dsDNA CTS 4 pmol [CD5-NGS-revision-VVPlate-1C04_S27]


title: Hi-C_embryo_CTCF_0_rep2

description: Hi-C library

source_name: CTCF[0] 2-6 hour old embryos, rep2


title: DSP-1001660003683-G-B09

source_name: Pancreas


title: WT unwounded petiole sample under high R/FR from A. thaliana after 1h30 [1.3]

description:
ASF_1C
PolyA
Col.high.no_wound.1.3
processed data file: genes.counts.normalized.txt


title: Donor1 G472 RNP only - [CD5-NGS-revision-VVPlate-1C02_S11]

source_name: primary Bulk T human cells

value: G472 RNP only -


title: Hi-C_embryo_CTCF_0_rep1

description: Hi-C library

source_name: CTCF[0] 2-6 hour old embryos, rep1


title: Donor1 G472 CD5-HA dsDNA 4 pmol [CD5-NGS-revision-VVPlate-1C03_S19]

value: G472 CD5-HA dsDNA 4 pmol


title: aos unwounded petiole sample under low R/FR from A. thaliana after 4h [2.2]

description:
ASF_15B
PolyA
aos.low.no_wound.2.2
processed data file: genes.counts.normalized.txt

source_name: Petiole samples


title: Donor1 no electro No HDRT - [CD5-NGS-revision-VVPlate-1C01_S3]


title: DSP-1001660003683-G-A05


title: aos wounded petiole sample under high R/FR from A. thaliana after 1h30 [1.2]

description:
ASF_10B
PolyA
aos.high.wound.1.2
processed data file: genes.counts.normalized.txt


title: DSP-1001660003683-G-C01


title: aos unwounded petiole sample under low R/FR from A. thaliana after 1h30 [1.2]

description:
ASF_11B
PolyA
aos.low.no_wound.1.2
processed data file: genes.counts.normalized.txt


title: DSP-1001660003683-G-B10


title: Donor2 G472 CD5-HA ssDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-1B12_S90]

value: G472 CD5-HA ssDNA CTS 20 pmol


title: Hi-C_embryo_Cp190_0_rep4

description: Hi-C library

source_name: Cp190[0] 2-6 hour old embryos, rep4


title: DSP-1001660003683-G-A11


title: aos unwounded petiole sample under high R/FR from A. thaliana after 4h [2.2]

description:
ASF_13B
PolyA
aos.high.no_wound.2.2
processed data file: genes.counts.normalized.txt

value: high R/FR


title: Hi-C_embryo_Cp190_0_rep3

description: Hi-C library

source_name: Cp190[0] 2-6 hour old embryos, rep3


title: Donor2 G472 CD5-HA ssDNA 20 pmol [CD5-NGS-revision-VVPlate-1B11_S82]

value: G472 CD5-HA ssDNA 20 pmol


title: aos unwounded petiole sample under high R/FR from A. thaliana after 1h30 [1.2]

description:
ASF_9B
PolyA
aos.high.no_wound.1.2
processed data file: genes.counts.normalized.txt

value: no


title: DSP-1001660003683-G-B08


title: Hi-C_embryo_Cp190_0_rep2

description: Hi-C library

source_name: Cp190[0] 2-6 hour old embryos, rep2


title: Hi-C_embryo_Cp190_0_rep1

description: Hi-C library

source_name: Cp190[0] 2-6 hour old embryos, rep1


title: DSP-1001660003683-G-B02


title: Donor2 G472 CD5-HA dsDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-1B10_S74]

value: G472 CD5-HA dsDNA CTS 20 pmol


title: Donor2 G472 RNP only - [CD5-NGS-revision-VVPlate-1B08_S58]


title: DSP-1001660003683-G-B06


title: WT wounded petiole sample under low R/FR from A. thaliana after 1h30 [1.2]

description:
ASF_4B
PolyA
Col.low.wound.1.2
processed data file: genes.counts.normalized.txt

value: Petiole

value: low R/FR


title: Donor2 no electro No HDRT - [CD5-NGS-revision-VVPlate-1B07_S50]

value: primary Bulk T human cells

value: no electro No HDRT -


title: WT wounded petiole sample under high R/FR from A. thaliana after 4h [2.2]

description:
ASF_6B
PolyA
Col.high.wound.2.2
processed data file: genes.counts.normalized.txt

value: 18 days post germination


title: Donor2 G472 CD5-HA dsDNA 20 pmol [CD5-NGS-revision-VVPlate-1B09_S66]

value: G472 CD5-HA dsDNA 20 pmol


title: WT unwounded petiole sample under low R/FR from A. thaliana after 4h [2.2]

description:
ASF_7B
PolyA
Col.low.no_wound.2.2
processed data file: genes.counts.normalized.txt


title: Cp190 ChIP, Cp190[KO] larval CNS, rep2

description: ChIP-seq library

data_processing:
Reads were aligned against Drosophila melanogaster genome assembly release 6 (dm6) using MicMap (v2.2)
For samples that were sequenced twice, reads were merged with Samtools v1.10.
Samtools v1.10 was used to identify duplicate reads
Coverage (in reads per million) was evaluated after truncating each paired end read to the 50nt region centered on the its midpoint, ignoring duplicate reads.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files were generated using R package rtracklayer v1.42.2. Score represent coverage in reads per million.

extract_protocol:
About 400 0-14 hour old embryos per biological replicate (three biological replicates prepared per genotype) were dechorionated, dounced in 5 ml crosslinking solution (50 mM Hepes pH 7.9, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 1.8% formaldehyde), and fixed for 15 minutes. Nuclei were sonicated in RIPA buffer in a Covaris S220 sonicator as described in Kaushal et al. 2021. 60 third instar larval central nervous systems per biological replicate (two biological replicates per genotype) were dissected in PBS and chromatin was prepared as in Kaushal et al. 2021.
NEBNext Ultra II DNA Library Prep kit for Illumina

value: central nervous system

value: wandering third instar larva

tag: replicate

tag: chip antibody

value: Cp190 rabbit polyclonal (Kaushal et al. 2021)


title: Cp190 ChIP, su(Hw)[KO] larval CNS, rep2

description: ChIP-seq library

source_name: third instar larval central nervous system

value: su(Hw)[KO]


title: WT wounded petiole sample under high R/FR from A. thaliana after 1h30 [1.2]

description:
ASF_2B
PolyA
Col.high.wound.1.2
processed data file: genes.counts.normalized.txt

value: WT

value: yes


title: DSP-1001660003683-G-A08

value: Pancreas

value: Untreated


title: Cp190 ChIP, WT larval CNS, rep2

description: ChIP-seq library

value: wildtype


title: Donor1 G472 CD5-HA ssDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-1B06_S42]

value: G472 CD5-HA ssDNA CTS 20 pmol


title: DSP-1001660003683-G-B04


title: Cp190 ChIP, su(Hw)[KO] larval CNS, rep1

description: ChIP-seq library


title: WT unwounded petiole sample under low R/FR from A. thaliana after 1h30 [1.2]

description:
ASF_3B
PolyA
Col.low.no_wound.1.2
processed data file: genes.counts.normalized.txt

value: no


title: DSP-1001660003683-G-A07


title: Cp190 ChIP, Cp190[KO] larval CNS, rep1

description: ChIP-seq library


title: DSP-1001660003683-G-B03


title: Donor1 G472 CD5-HA dsDNA CTS 20 pmol [CD5-NGS-revision-VVPlate-1B04_S26]

value: G472 CD5-HA dsDNA CTS 20 pmol


title: CTCF ChIP, WT[0], rep3

description: ChIP-seq library

source_name: 0-14 hour old embryos

value: WT[0] (matched wildtype control)

value: whole embryo

value: 0-14 hour old

value: CTCF rabbit polyclonal (Kaushal et al. 2021)


title: WT wounded petiole sample under low R/FR from A. thaliana after 4h [2.2]

description:
ASF_8B
PolyA
Col.low.wound.2.2
processed data file: genes.counts.normalized.txt

value: Petiole

value: 18 days post germination

value: low R/FR


title: Cp190 ChIP, WT larval CNS, rep1

description: ChIP-seq library

value: central nervous system

value: wandering third instar larva

value: Cp190 rabbit polyclonal (Kaushal et al. 2021)


title: DSP-1001660003683-G-B05


title: Donor1 G472 CD5-HA dsDNA 20 pmol [CD5-NGS-revision-VVPlate-1B03_S18]

value: primary Bulk T human cells

value: G472 CD5-HA dsDNA 20 pmol


title: WT unwounded petiole sample under high R/FR from A. thaliana after 4h [2.2]

description:
ASF_5B
PolyA
Col.high.no_wound.2.2
processed data file: genes.counts.normalized.txt

value: WT

value: high R/FR


title: CTCF ChIP, WT[0], rep2

description: ChIP-seq library


title: Donor1 G472 CD5-HA ssDNA 20 pmol [CD5-NGS-revision-VVPlate-1B05_S34]

value: G472 CD5-HA ssDNA 20 pmol


title: Donor1 no electro No HDRT - [CD5-NGS-revision-VVPlate-1B01_S2]

value: no electro No HDRT -


title: DSP-1001660003683-G-A01

value: Pancreas

value: No Template Control


title: Donor2 G472 CD5-HA ssDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-1A12_S89]

value: G472 CD5-HA ssDNA CTS 100 pmol


title: aos wounded petiole sample under low R/FR from A. thaliana after 1h30 [1.1]

description:
ASF_12A
PolyA
aos.low.wound.1.1
processed data file: genes.counts.normalized.txt

value: aos

value: yes


title: WT unwounded petiole sample under high R/FR from A. thaliana after 1h30 [1.2]

description:
ASF_1B
PolyA
Col.high.no_wound.1.2
processed data file: genes.counts.normalized.txt

value: Petiole

value: no


title: CTCF ChIP, CTCF[0], rep3

description: ChIP-seq library

value: whole embryo

value: 0-14 hour old

value: CTCF rabbit polyclonal (Kaushal et al. 2021)


title: aos wounded petiole sample under low R/FR from A. thaliana after 4h [2.1]

description:
ASF_16A
PolyA
aos.low.wound.2.1
processed data file: genes.counts.normalized.txt

value: 18 days post germination

value: low R/FR


title: aos wounded petiole sample under high R/FR from A. thaliana after 4h [2.1]

description:
ASF_14A
PolyA
aos.high.wound.2.1
processed data file: genes.counts.normalized.txt


title: CTCF ChIP, WT[0], rep1

description: ChIP-seq library

value: WT[0] (matched wildtype control)


title: DSP-1001660003683-G-A12

value: Untreated


title: Donor2 G472 CD5-HA ssDNA 100 pmol [CD5-NGS-revision-VVPlate-1A11_S81]

value: primary Bulk T human cells

value: G472 CD5-HA ssDNA 100 pmol


title: aos wounded petiole sample under high R/FR from A. thaliana after 1h30 [1.1]

description:
ASF_10A
PolyA
aos.high.wound.1.1
processed data file: genes.counts.normalized.txt

value: high R/FR


title: DSP-1001660003683-G-A04

value: Pancreas


title: CTCF ChIP, CTCF[0], rep2

description: ChIP-seq library


title: DSP-1001660003683-G-A03


title: CTCF ChIP, CTCF[0], rep1

description: ChIP-seq library


title: CTCF ChIP, Cp190[0], rep3

description: ChIP-seq library


title: Donor2 G472 CD5-HA dsDNA 100 pmol [CD5-NGS-revision-VVPlate-1A09_S65]

value: G472 CD5-HA dsDNA 100 pmol


title: Kidney organoids 11mM glucose 1dpi SARS-CoV-2

city: Pamplona

first: Asier

last: Ullate-Agote

state: Navarra

address: Av. de Pío XII, 55

department: Hemato-Oncology

institute: CIMA

data_processing:
Demultiplexing, alignment to the Homo sapiens (hg38) genome and quantification using the annotation from Ensembl v93 was performed using 10X Genomics Cell Ranger (v4.0.0)
Downstream analysis steps (quality control filtering, normalization, integration, clustering and differential expression) were performed using the R package Seurat (v3.2.1)
Genome_build: hg38
Supplementary_files_format_and_content: HDF5 Feature Barcode Matrix containing a Gene x Cells UMI count matrix

molecule: polyA RNA

source_name: Human Kidney Organoid

growth_protocol: hPSCs were maintained in Essential 8 medium (Life Technologies #A1517001) in p10 culture plates coated with vitronectin (Fisher Scientific S.L. A14700) in a 37ºC incubator with 5% CO2 and were passaged every 5-6 days.

extract_protocol:
After the indicated treatments kidney organoids were collected and washed twice with PBS, and further dissociated into a single cell suspension by treating them with Accumax (07921, Stem Cell Technologies) for 15 min at 37ºC followed by Trypsin-EDTA 0.25% (wt/vol) trypsin (25300-054, Life Technologies)  for additional 15 min at 37ºC. The reaction was deactivated by adding 10% FBS. The cell suspension was then passed through a 40μm cell strainer. After centrifugation at 1,000 RPM for 5 minutes cell numbers and viability were analyzed using Countess Automated Cell Counter (Invitrogen). This method generated single cell suspension with greater than 90% viability. Cell suspensions were frozen until further use. For library construction cells were thawed and centrifuged at 1,000 RPM for 5 minutes. Cell numbers and viability were analyzed using Countess Automated Cell Counter (Invitrogen) and cell suspensions were loaded onto a well of a 10X Chromium Single Cell instrument. Barcoding and cDNA synthesis were performed according to the manufacturer´s instructions. The cDNA libraries were constructed using the 10X Chromium Single cell 3' Library Kit v3 according to the manufacturer's original protocol and sequenced either with a NovaSeq 6000 (R1:28,R2:94,i7:8) or a NextSeq 500 (R1:28, R2:55, i7:8) instrument.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hPSCs grown on vitronectin were washed twice with PBS (Life Technologies #1001-015) and dissociated into small clusters with EDTA (Sigma #E9884). Cells were then seeded onto vitronectin pre-coated culture dishes at a density of 50.000-150.000 cells per cm2 in Essential 8 Medium. After overnight culture, the differentiation was initiated (day -4) by treatment with 8µM CHIR99021 (Sigma #SML1046-5MG) in basic differentiation medium [Advanced RPMI 1640(Life technologies #12633-012) + 1 × 1-GlutaMAX (Life Technologies #35050-038) + Penicillin/Streptomycin (Life Technologies #15140122)] for 3 days. On day -1, CHIR99021 was removed by washing once with PBS and cells were exposed to 200 ng ml-1 FGF9 (PeproTech House#100-23B), 1 µ ml -1 Heparin (Sigma#H3149-10KU) and 10 ng ml-1 Activin A (Vitro S.A #338-AC-050) in basic differentiation media for 24h. On day 0, cells were mechanically dissociated into single cells and resuspended in basic differentiation medium supplemented with 3μM CHIR99021, 200 ng ml-1 FGF9 and 1µg ml-1 Heparin. Cells were then placed in 96-well, round bottom, ultra-low attachment plates at a density of 500.000 cells per well. Cells were spun down at x300g for 2 min form a pellet and then cultured at 37ºC, 5% CO2 for 2 days additional days without media change. On day 2, the pellets were transferred onto a Transwell 0.4µm pore polyester membrane (Sigma#3460) and treated with basic differentiation media supplemented with 3μM CHIR99021, 200 ng ml-1 FGF9 and 1µg ml-1 Heparin. On day 3, CHIR99021 was removed and the organoids were switched to basic differentiation media supplemented with 200 ng ml-1 FGF9 and 1µg ml-1 Heparin for another 4 days. From that point, organoids were cultured in basic differentiation medium and maintained without additional growth factors. For experiments employing glucose challenge, day 16 kidney organoids were diexposed to low glucose DMEM (ThermoFisher) supplemented with 1% Penicillin-Streptomycin for 6h (starvation period). After this time, normoglycemic conditions were assessed exposing organoids into DMEM supplemented with 5mM D-Glucose changing medium every day until day 23. Hyperglycaemic-like organoids were incubated with DMEM supplemented with 5mM D-Glucose on even days or with 25mM of D-Glucose on odd days until day 23 (5-25mM oscillatory hyperglycaemic condition).

value: kidney organoid

value: 11mM glucose

tag: infection

value: SARS-CoV-2 infection


title: Kidney organoids 11mM glucose mock

tag: tissue

value: mock


title: aos unwounded petiole sample under high R/FR from A. thaliana after 1h30 [1.1]

description:
ASF_9A
PolyA
aos.high.no_wound.1.1
processed data file: genes.counts.normalized.txt

value: aos

value: Petiole

value: no

tag: time


title: Cp190 ChIP, WT[0], rep3

description: ChIP-seq library

value: whole embryo

value: 0-14 hour old

value: Cp190 rabbit polyclonal (Kaushal et al. 2021)


title: aos unwounded petiole sample under high R/FR from A. thaliana after 4h [2.1]

description:
ASF_13A
PolyA
aos.high.no_wound.2.1
processed data file: genes.counts.normalized.txt

value: 18 days post germination


title: Kidney organoids 5mM glucose 1dpi SARS-CoV-2

value: 5mM glucose


title: Donor1 G472 RNP only - [CD5-NGS-revision-VVPlate-1B02_S10]

value: primary Bulk T human cells

value: G472 RNP only -


title: Cp190 ChIP, WT[0], rep2

description: ChIP-seq library

value: WT[0] (matched wildtype control)


title: Donor1 G472 CD5-HA ssDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-1A06_S41]

value: G472 CD5-HA ssDNA CTS 100 pmol


title: Donor2 G472 RNP only - [CD5-NGS-revision-VVPlate-1A08_S57]


title: aos unwounded petiole sample under low R/FR from A. thaliana after 1h30 [1.1]

description:
ASF_11A
PolyA
aos.low.no_wound.1.1
processed data file: genes.counts.normalized.txt

value: low R/FR


title: Kidney organoids 5mM glucose mock

value: kidney organoid


title: Kidney organoids 5-25mM oscillatory glucose 1dpi SARS-CoV-2

value: 5-25mM oscillatory glucose every 12h


title: WT wounded petiole sample under low R/FR from A. thaliana after 4h [2.1]

description:
ASF_8A
PolyA
Col.low.wound.2.1
processed data file: genes.counts.normalized.txt

value: WT

value: yes


title: Kidney organoids 5-25mM oscillatory glucose mock

value: mock


title: Donor2 no electro No HDRT - [CD5-NGS-revision-VVPlate-1A07_S49]

value: no electro No HDRT -


title: Cp190 ChIP, CTCF[0], rep3

description: ChIP-seq library


title: Donor2 G472 CD5-HA dsDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-1A10_S73]

value: G472 CD5-HA dsDNA CTS 100 pmol


title: aos unwounded petiole sample under low R/FR from A. thaliana after 4h [2.1]

description:
ASF_15A
PolyA
aos.low.no_wound.2.1
processed data file: genes.counts.normalized.txt

value: aos

value: Petiole

value: no


title: Donor1 G472 CD5-HA dsDNA 100 pmol [CD5-NGS-revision-VVPlate-1A03_S17]

value: G472 CD5-HA dsDNA 100 pmol


title: Donor1 G472 CD5-HA ssDNA 100 pmol [CD5-NGS-revision-VVPlate-1A05_S33]

value: G472 CD5-HA ssDNA 100 pmol


title: WT Dark Rep 3

city: Oxford

first: Luis

last: Actis

address: E High St

department: Microbiology

institute: Miami University

data_processing:
Sequencing protocol is deatiled in NovaSeq 6000 System User Guide Document # 1000000019358 v02. Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences using FastQC v0.11.7 and Trimmomatic 0.38
Then reads were mapped to the reference sequence using Bowtie 1.1.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al.. Data was transformed and normalized using edgeR R library to trimmed Mean of M-values (TMM)
Reads were further processed for differenitial gene expression and functional annotation using HTSeq 0.10.0 and KEGG
Supplementary_files_format_and_content: text file with appropriate column names including feature_id, chromosome and location (strand, start, end), type, locus_tag (new and old), gene name, protein_id, possible product, counts, and normalized RPKM

organism: Acinetobacter baumannii ATCC 17978

source_name: bacterial RNA

growth_protocol: Bacterial cultures were cultured in swimming broth (SB) composed of 1% tryptone and 0.5% NaCl with 3 independent biological replicates per treatment. Overnight cultures were diluted 1:100 in SB and then grown at 37ºC with shaking at 150 rpm to an OD600 of appromixmately 0.8.

extract_protocol:
Three independent biological replicates per illumination and darkness were used for extraction using Zymo's Direct-zol RNA Miniprep Plus kit. 1 mL of culture were pelleted by centrifugation and then lysed using the TRIzol reagent for each sample. DNA contamination and RNA quality were checked before samples were sent to psomagen for library preparation and cDNA sequencing.
Psomagen used the TruSeq stranded Total RNA kit with the Novaseq 6000 S4 Reagent Kit.  Htseq 0.10.0 was used for sequence analysis with NCBI NZ_CP012004 and NZ_CP012005.1 being used as reference sequences.

treatment_protocol: RNA was extracted from overnight bacterial cultures grown at 37ºC under darkness or illumination (LED array with peak emission wavelength of 469 nm) shaking at 150 rpm to an OD600 of about 0.8.

value: dark

value: wild type

value: bacterial


title: Donor1 G472 RNP only - [CD5-NGS-revision-VVPlate-1A02_S9]

value: primary Bulk T human cells

value: G472 RNP only -


title: Donor1 G472 CD5-HA dsDNA CTS 100 pmol [CD5-NGS-revision-VVPlate-1A04_S25]


title: WT unwounded petiole sample under low R/FR from A. thaliana after 1h30 [1.1]

description:
ASF_3A
PolyA
Col.low.no_wound.1.1
processed data file: genes.counts.normalized.txt

value: 18 days post germination

value: low R/FR


title: Donor1 no electro No HDRT - No inhibitor [CD5-NGS-revision-VVPlate-1A01_S1]

value: no electro No HDRT - No inhibitor


title: WT wounded petiole sample under high R/FR from A. thaliana after 4h [2.1]

description:
ASF_6A
PolyA
Col.high.wound.2.1
processed data file: genes.counts.normalized.txt

value: WT

value: high R/FR

value: yes


title: WT Dark Rep 2


title: WT unwounded petiole sample under high R/FR from A. thaliana after 4h [2.1]

description:
ASF_5A
PolyA
Col.high.no_wound.2.1
processed data file: genes.counts.normalized.txt


title: Zymo microbial standard - PCR

city: Houston

first: Tao

middle: P.

last: Wu

state: TX

address: One Baylor Plaza, MS BCM225

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Library strategy: NT-seq
sequencing reads were trimmed using cutadapt (v1.18) to remove adaptors. Duplicated reads were removed using BBMAP (v38.84)34 clumpify package.
Fastq reads and fasta reference were converted to AT-only format (convert all purine to A and all thymine to T). Converted fastq reads were aligned to reference using bowtie2 (v2.3.5.1)
AT only sam files were converted back to sam files with original reads using custom python scripts. NM and MD tags were recalculated using samtools (1.9) calmd. The alignments in sam files were filtered by recreated MD tag to keep allowed base mutation (A to G and C to T)
Base count at each genomic location was generated by igvtools (v2.5.3)
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Comma-separated values

organism: mixed culture metagenome

source_name: microbial community

extract_protocol:
Genomic DNA was extrated using DNeasy Blood and Tissue Kit according to the manufacturer's instructions (Qiagen, 69506)
Genomic DNA was fragmentized to 100-300 bp using Covaris S220 Focused-ultrasonicator. Fragmented gDNA was ligated to TruSeq adaptor using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645S). Unmodified control DNA was made by amplifying adaptor-ligated DNA using Q5 DNA polymerase (NEB, M0492S). Nitrite treatment was performed in both native and amplified DNA. Indexed libraries were constructed using NEB ultra ii library prep kit.

value: wild-type


title: Zymo microbial standard - native


title: CTCF ChIP, Cp190[0], rep2

description: ChIP-seq library

value: whole embryo

value: 0-14 hour old

value: CTCF rabbit polyclonal (Kaushal et al. 2021)


title: Cp190 ChIP, CTCF[0], rep2

description: ChIP-seq library

value: Cp190 rabbit polyclonal (Kaushal et al. 2021)


title: WT wounded petiole sample under high R/FR from A. thaliana after 1h30 [1.1]

description:
ASF_2A
PolyA
Col.high.wound.1.1
processed data file: genes.counts.normalized.txt

value: Petiole


title: lung single cell 384

status: Public on May 11 2022

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description:
lung single cell 384
898s_P9

data_processing:
The sequencing reads were first aligned to the mouse reference genome GRCm38 (mm10) with tophat (version 2.1.1). The duplicated reads were removed using samtools software (version 0.1.18). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample

source_name: Lung

extract_protocol:
A 12 week-old female Prox1-GFP mouse was perfused with PBS to clear the blood. Subsequently, the lung was filled with 10 mg mL-1 dispase II in PBS via the trachea and incubated for 10 min at RT. Next, 1.0 mg mL-1 collagenase II in PBS supplemented with 0.2 mg mL-1 DNase I was injected into the lung lobes and lung tissue was minced with scissors in 1.5 mL of 1.0 mg mL-1 collagenase II in PBS supplemented with 0.2 mg mL-1 DNase I. Tissue dissociation was performed for 15 min at 37°C and 750 rpm. Digests were quenched by the addition of 2 mM EDTA f.c., filtered through a 40 µm nylon filter, washed with FACS buffer (PBS, 0.5% FBS, and 2 mM EDTA) for 5 min at 300 g, RT and processed for FACS sorting. Briefly,  Fc-receptor binding was blocked with rat anti-mouse CD16/CD32 for 10 min on ice. Thereafter, samples were incubated with fluorophore-conjugated anti-CD31 (clone 390, 1.0 µg mL-1), anti-CD45 (clone 30-F11, 4 µg mL-1), anti-CD11b (clone M1/70, 4 µg mL-1) and anti-TER-119 (clone TER-119, 4 µg mL-1) antibodies for 20 min on ice. Prior to sorting of CD31+ Prox1-GFP+ CD45- CD11b- Ter119- lymphatic and CD31+ Prox1-GFP- CD45- CD11b- Ter119- blood endothelial cells on a BD FACS Aria III samples were again filtered through a 40 µm filter and supplemented with 1 µM SytoxBlue to label dead cells.
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

value: lung

value: adult mice


title: WT Dark Rep 1

value: dark

value: wild type

value: bacterial


title: lung single cell 382

description:
lung single cell 382
898s_P7


title: Cp190 ChIP, WT[0], rep1

description: ChIP-seq library

value: WT[0] (matched wildtype control)


title: WT unwounded petiole sample under low R/FR from A. thaliana after 4h [2.1]

description:
ASF_7A
PolyA
Col.low.no_wound.2.1
processed data file: genes.counts.normalized.txt

value: 18 days post germination

value: low R/FR

value: no


title: Cp190 ChIP, CTCF[0], rep1

description: ChIP-seq library


title: Cp190 ChIP, Cp190[0], rep3

description: ChIP-seq library


title: WT Light Rep 3

value: illumination


title: lung single cell 381

description:
lung single cell 381
898s_P6


title: WT wounded petiole sample under low R/FR from A. thaliana after 1h30 [1.1]

description:
ASF_4A
PolyA
Col.low.wound.1.1
processed data file: genes.counts.normalized.txt

value: WT

value: yes


title: WT Light Rep 2


title: lung single cell 376

description:
lung single cell 376
898s_P24


title: lung single cell 374

description:
lung single cell 374
898s_P22


title: lung single cell 378

description:
lung single cell 378
898s_P3


title: lung single cell 373

description:
lung single cell 373
898s_P21


title: WT Light Rep 1


title: lung single cell 383

description:
lung single cell 383
898s_P8


title: lung single cell 371

description:
lung single cell 371
898s_P1


title: lung single cell 372

description:
lung single cell 372
898s_P20


title: WT unwounded petiole sample under high R/FR from A. thaliana after 1h30 [1.1]

description:
ASF_1A
PolyA
Col.high.no_wound.1.1
processed data file: genes.counts.normalized.txt

value: high R/FR


title: lung single cell 367

description:
lung single cell 367
898s_P16


title: lung single cell 366

description:
lung single cell 366
898s_P15


title: lung single cell 380

description:
lung single cell 380
898s_P5


title: lung single cell 361

description:
lung single cell 361
898s_P10


title: lung single cell 357

description:
lung single cell 357
898s_O6


title: lung single cell 375

description:
lung single cell 375
898s_P23


title: Cp190 ChIP, Cp190[0], rep2

description: ChIP-seq library

value: whole embryo

value: 0-14 hour old


title: lung single cell 355

description:
lung single cell 355
898s_O4


title: lung single cell 350

description:
lung single cell 350
898s_O22


title: lung single cell 349

description:
lung single cell 349
898s_O21


title: lung single cell 377

description:
lung single cell 377
898s_P2


title: lung single cell 363

description:
lung single cell 363
898s_P12


title: Cp190 ChIP, Cp190[0], rep1

description: ChIP-seq library

value: Cp190 rabbit polyclonal (Kaushal et al. 2021)


title: lung single cell 347

description:
lung single cell 347
898s_O1


title: lung single cell 364

description:
lung single cell 364
898s_P13


title: lung single cell 345

description:
lung single cell 345
898s_O18


title: lung single cell 379

description:
lung single cell 379
898s_P4


title: lung single cell 368

description:
lung single cell 368
898s_P17


title: lung single cell 365

description:
lung single cell 365
898s_P14


title: lung single cell 359

description:
lung single cell 359
898s_O8


title: lung single cell 360

description:
lung single cell 360
898s_O9


title: lung single cell 358

description:
lung single cell 358
898s_O7


title: lung single cell 369

description:
lung single cell 369
898s_P18


title: lung single cell 354

description:
lung single cell 354
898s_O3


title: lung single cell 370

description:
lung single cell 370
898s_P19


title: lung single cell 348

description:
lung single cell 348
898s_O20


title: lung single cell 341

description:
lung single cell 341
898s_O14


title: lung single cell 356

description:
lung single cell 356
898s_O5


title: lung single cell 353

description:
lung single cell 353
898s_O2


title: lung single cell 337

description:
lung single cell 337
898s_O10


title: lung single cell 351

description:
lung single cell 351
898s_O23


title: lung single cell 334

description:
lung single cell 334
898s_N7


title: lung single cell 333

description:
lung single cell 333
898s_N6


title: lung single cell 336

description:
lung single cell 336
898s_N9


title: lung single cell 346

description:
lung single cell 346
898s_O19


title: lung single cell 331

description:
lung single cell 331
898s_N4


title: lung single cell 335

description:
lung single cell 335
898s_N8


title: lung single cell 329

description:
lung single cell 329
898s_N2


title: lung single cell 328

description:
lung single cell 328
898s_N24


title: lung single cell 339

description:
lung single cell 339
898s_O12


title: lung single cell 340

description:
lung single cell 340
898s_O13


title: lung single cell 324

description:
lung single cell 324
898s_N20


title: lung single cell 342

description:
lung single cell 342
898s_O15


title: lung single cell 362

description:
lung single cell 362
898s_P11


title: lung single cell 352

description:
lung single cell 352
898s_O24


title: lung single cell 323

description:
lung single cell 323
898s_N1


title: lung single cell 338

description:
lung single cell 338
898s_O11


title: lung single cell 344

description:
lung single cell 344
898s_O17


title: lung single cell 317

description:
lung single cell 317
898s_N14


title: lung single cell 332

description:
lung single cell 332
898s_N5


title: lung single cell 343

description:
lung single cell 343
898s_O16


title: lung single cell 312

description:
lung single cell 312
898s_M9


title: lung single cell 327

description:
lung single cell 327
898s_N23


title: lung single cell 326

description:
lung single cell 326
898s_N22


title: lung single cell 311

description:
lung single cell 311
898s_M8


title: lung single cell 330

description:
lung single cell 330
898s_N3


title: lung single cell 320

description:
lung single cell 320
898s_N17


title: lung single cell 322

description:
lung single cell 322
898s_N19


title: lung single cell 321

description:
lung single cell 321
898s_N18


title: lung single cell 302

description:
lung single cell 302
898s_M22


title: lung single cell 318

description:
lung single cell 318
898s_N15


title: lung single cell 325

description:
lung single cell 325
898s_N21


title: lung single cell 319

description:
lung single cell 319
898s_N16


title: lung single cell 316

description:
lung single cell 316
898s_N13


title: lung single cell 315

description:
lung single cell 315
898s_N12


title: lung single cell 314

description:
lung single cell 314
898s_N11


title: lung single cell 307

description:
lung single cell 307
898s_M4


title: lung single cell 308

description:
lung single cell 308
898s_M5


title: lung single cell 310

description:
lung single cell 310
898s_M7


title: lung single cell 304

description:
lung single cell 304
898s_M24


title: lung single cell 306

description:
lung single cell 306
898s_M3


title: lung single cell 309

description:
lung single cell 309
898s_M6


title: lung single cell 305

description:
lung single cell 305
898s_M2


title: lung single cell 296

description:
lung single cell 296
898s_M17


title: lung single cell 297

description:
lung single cell 297
898s_M18


title: lung single cell 300

description:
lung single cell 300
898s_M20


title: lung single cell 292

description:
lung single cell 292
898s_M13


title: lung single cell 293

description:
lung single cell 293
898s_M14


title: lung single cell 294

description:
lung single cell 294
898s_M15


title: lung single cell 301

description:
lung single cell 301
898s_M21


title: lung single cell 298

description:
lung single cell 298
898s_M19


title: lung single cell 295

description:
lung single cell 295
898s_M16


title: lung single cell 299

description:
lung single cell 299
898s_M1


title: lung single cell 290

description:
lung single cell 290
898s_M11


title: lung single cell 291

description:
lung single cell 291
898s_M12


title: lung single cell 286

description:
lung single cell 286
898s_L7


title: lung single cell 287

description:
lung single cell 287
898s_L8


title: lung single cell 281

description:
lung single cell 281
898s_L2


title: lung single cell 289

description:
lung single cell 289
898s_M10


title: lung single cell 283

description:
lung single cell 283
898s_L4


title: lung single cell 284

description:
lung single cell 284
898s_L5


title: lung single cell 285

description:
lung single cell 285
898s_L6


title: XF 987_AltN172

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

department: Immunology

country: France

institute: Institut Pasteur

data_processing:
Standard basecalling formats for Nextseq reads
Nexteq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Assembly: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)
Library strategy: CSR-HTGTS-Seq

source_name: Mouse splenic B cells

extract_protocol:
DNA was extracted overnight at 56 degree Celcius in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using CSR-HTGTS-Seq (Dong et al., 2015)

treatment_protocol: Splenic B cells were cultured in lymphocyte medium R15 stimulated with aIgD-dextran/LPS/IL4

value: splenic B cells

tag: activation

tag: treatment protocol

value: cytokine stimulation

tag: target locus

value: Single CBE insertion with the same orientation as 3'CBEs in non-coding IgH Sm-Sa deletion cells

tag: growth conditions


title: XF 986_AltN172

tag: cell type


title: lung single cell 280

description:
lung single cell 280
898s_L24

tag: strain

value: lung

value: adult mice


title: XF 985_AltN172


title: XF 984_AltN172

value: non-coding IgH Sm-Sa deletion


title: lung single cell 282

description:
lung single cell 282
898s_L3


title: XF 983_AltN172


title: lung single cell 288

description:
lung single cell 288
898s_L9


title: lung single cell 278

description:
lung single cell 278
898s_L22


title: lung single cell 279

description:
lung single cell 279
898s_L23


title: lung single cell 277

description:
lung single cell 277
898s_L21


title: lung single cell 276

description:
lung single cell 276
898s_L20


title: lung single cell 272

description:
lung single cell 272
898s_L17


title: XF 981_AltN171

value: three CBEs insertion downstream of Cg2a in Ia deleted cells


title: lung single cell 273

description:
lung single cell 273
898s_L18


title: lung single cell 274

description:
lung single cell 274
898s_L19


title: XF 982_AltN172


title: XF 977_AltN171

value: XLF-/-

value: Ia deletion in non-coding IgH Sm-Sa deletion cells


title: XF 978_AltN171


title: XF 979_AltN171


title: XF 980_AltN171


title: lung single cell 270

description:
lung single cell 270
898s_L15


title: XF 976_AltN171


title: lung single cell 269

description:
lung single cell 269
898s_L14


title: XF 975_AltN171


title: lung single cell 275

description:
lung single cell 275
898s_L1


title: XF 972_AltN171


title: XF 974_AltN171


title: lung single cell 268

description:
lung single cell 268
898s_L13


title: lung single cell 265

description:
lung single cell 265
898s_L10


title: lung single cell 264

description:
lung single cell 264
898s_K9


title: XF 973_AltN171


title: lung single cell 267

description:
lung single cell 267
898s_L12


title: lung single cell 266

description:
lung single cell 266
898s_L11


title: XF 971_AltN171


title: Aged OPCs Aged CSF 16hr sample 4

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

data_processing:
Each experimental setup was processed as described below:
1. Raw sequencing files were demultiplexed with bcl2fastq, reads were aligned using STAR, and counts of technical replicates were summed up using DESeq2 before performing normalization and differential expression analysis with standard settings.
2. Sequencing quality control was performed using FastQC v0.11.8 and summary reports were generated with MultiQC v1.7. FASTQ files were then analyzed using the SLAM-DUNK pipeline v0.3.4 and the related alleyoop toolchain. The pipeline comprises 1) read mapping, 2) alignment filtering, 3) SNP calling and correction, and 4) 3'-UTR sequence counting. Using NextGenMap reads were aligned against the genome of Rattus norvegicus (release 6.0), which was downloaded in FASTA format from Ensembl release v97. For mapping the following parameters were set; '-5 12, -a 4, -n 1, -ss' leaving rest at default. Resulting Binary sequence Alignment/Map (BAM) format files were filtered to remove low-quality alignments using the parameters '-mq 2, -mi 0.95, -nm -1’ and rest at default. Next, SNPs in alignments, in particular the T to C (T>C) conversions, were called with parameters '-c 10, -f 0.8' and others remaining at default. Statistical independence of distributions of true SNP-callings identified by VarScan2 in relation to the number of T>C reads was assessed with a Mann-Whitney-U test for each sample as initially described in the alleyoop snpeval toolchain module. For the reference set of 3'-UTRs, a genome feature file (GFF3) for the Rattus norvegicus genome (release 6.0) was downloaded from Ensembl release v97, filtered to retain only three_prime_utr features and converted to Browser Extensible Data (BED) format using bedops v2.4.36. The BED file was used in combination with parameters '-c 1, -q 27' for the SLAMDUNK count command, leaving other parameters at default. Resulting 3'-UTR T>C and total read counts were added up on gene-level along all transcripts and alternative 3'-UTRs available per transcript. Entire down-stream analysis was performed using R v3.6.1, data.table v1.12.2, and common tidyverse packages (tidyr, dplyr, purrr, stringr, ggplot2). Differential gene expression analysis was carried out using DESeq2 v1.26.0 on the T>C count and total count matrices separately with standard settings with alpha level set to 0.05. In total, six DESeq2 experiments were performed, two with pooled timepoints (1hr + 6hr) per read-type (design variables Treatment and Time) and four with separate timepoint per read-type (design variable Treatment only). Effect size was calculated using the implementation of cohen’s d from the effsize v0.7.6 package. Gene set enrichment and over-representation analyses were performed using GeneTrail 3.0 65. Category source databases were adjusted independently, and P-values were corrected using the false discovery rate controlling procedure by Benjamini-Hochberg and considered significant if smaller than 0.05.
3. Libraries were sequenced to a depth of at least >10 million reads per sample. Raw sequencing files were demultiplexed and known adapters were trimmed with bcl2fastq. Data analysis of raw sequencing data was performed using the nextflow-core RNA-seq pipeline v3.0. Briefly, the core workflow of the pipeline maps filtered reads against the species reference genome using STAR and computes transcript counts using RSEM. For nuclear RNA-seq data, a custom reference genome was created where exon sequences in GTF files were modified to include all introns per transcript and used for the mapping instead. For mouse and rat sequencing data the reference genome GRCm38 and Rnor 6.0 provided by Illumina igenomes were used, respectively. All gene annotations were based on the ensembl database. Obtained raw gene transcript counts per sample were loaded into DESeq2, performing normalization for transcript length and sequencing depth, and differential expression analysis with standard settings. Effect sizes for each gene were computed based on normalized counts computed by DESeq2 using the function cohen.d of the R package effsize. Gene set enrichment analysis was performed using GeneTrail 3 using BH-FDR p-value adjustment with all remaining parameters kept at default.
4. Libraries were sequenced to a depth of at least >10 million reads per sample. Raw sequencing files were demultiplexed and known adapters were trimmed with bcl2fastq. Data analysis of raw sequencing data was performed using the nextflow-core RNA-seq pipeline v3.0. Briefly, the core workflow of the pipeline maps filtered reads against the species reference genome using STAR and computes transcript counts using RSEM. For nuclear RNA-seq data, a custom reference genome was created where exon sequences in GTF files were modified to include all introns per transcript and used for the mapping instead. For mouse and rat sequencing data the reference genome GRCm38 and Rnor 6.0 provided by Illumina igenomes were used, respectively. All gene annotations were based on the ensembl database. Obtained raw gene transcript counts per sample were loaded into DESeq2, performing normalization for transcript length and sequencing depth, and differential expression analysis with standard settings. Effect sizes for each gene were computed based on normalized counts computed by DESeq2 using the function cohen.d of the R package effsize. Gene set enrichment analysis was performed using GeneTrail 3 using BH-FDR p-value adjustment with all remaining parameters kept at default.
5. Libraries were sequenced to a depth of at least >10 million reads per sample. Raw sequencing files were demultiplexed and known adapters were trimmed with bcl2fastq. Data analysis of raw sequencing data was performed using the nextflow-core RNA-seq pipeline v3.0. Briefly, the core workflow of the pipeline maps filtered reads against the species reference genome using STAR and computes transcript counts using RSEM. For nuclear RNA-seq data, a custom reference genome was created where exon sequences in GTF files were modified to include all introns per transcript and used for the mapping instead. For mouse and rat sequencing data the reference genome GRCm38 and Rnor 6.0 provided by Illumina igenomes were used, respectively. All gene annotations were based on the ensembl database. Obtained raw gene transcript counts per sample were loaded into DESeq2, performing normalization for transcript length and sequencing depth, and differential expression analysis with standard settings. Effect sizes for each gene were computed based on normalized counts computed by DESeq2 using the function cohen.d of the R package effsize. Gene set enrichment analysis was performed using GeneTrail 3 using BH-FDR p-value adjustment with all remaining parameters kept at default.
Genome_build: GRCm38, Rnor_6.0.97
Supplementary_files_format_and_content: For each sample raw gene counts are provided. For SLAM-seq samples also the raw T-to-C counts are provided.

molecule: nuclear RNA

growth_protocol: Aged C57BL6 mice.

extract_protocol:
Nuclei isolation from frozen dissected hippocampi was done using the Nuclei EZ Prep Kit (Sigma-Aldrich, St. Louis, USA). Following the final PBS wash, nuclei were pelleted and resuspended in 100 μl of antibody mix (1:100, Anti-NeuN antibody-Alexa Fluor® 647, EPR12763, and 1:100, Anti-Olig2 antibody-Alexa Fluor® 488) with 0.2U/μl RNAse Inhibitor (Takara, 23138) in FACS buffer (0.5% BSA in PBS) and incubated on ice with intermittent shaking for 30 min. Nuclei were washed with 1ml FACS buffer and pelleted by centrifugation at 500 r.c.f. for 5 min, resuspended in FACS buffer with 0.2U/μl RNAse Inhibitor and Hoechst 33342 (1:2000, H3570, Thermo) and sorted on a Sony Sorter (SH800) based on Houechst+ NeuN- Olig2+high (OPC) and Houechst+ NeuN- Olig2+low (OL) gating to 350μl of RTL buffer and stored in -80°C until RNA extraction.
RNA was extracted with the RNeasy Plus Micro kit (Qiagen, 74034). cDNA and library synthesis were done inhouse using the Smart-seq2 protocol as previously described (Schaum, N. et al. Ageing hallmarks exhibit organ-specific temporal signatures. Nature (2020)), detailed protocol at https://doi-org.laneproxy.stanford.edu/10.17504/protocols.io.2uvgew6) with several modifications. Due to the low input RNA content, 2μl of RNA extracted from sorted nuclei was reversed transcribed using 16 cycles for OL samples and 18 cycles for OPC samples. Following bead cleanup using 0.7x ratio with AMPure beads (A63881, Fisher), cDNA concentration was measured using the Qubit 1x dsDNA HS kit (Q33231) and normalized to 0.4 ng/µl as input for library prep. 0.4 μl of each normalized sample was mixed with 1.2 μl of Tn5 Tagmentation mix (0.64 μl TAPS-PEG buffer (PEG 8000, V3011 , PROMEGA, and TAPS-NaOH pH8.5, BB-2375, Boston Bioproducts), 0.46 μl H2O and 0.1 μl Tn5 enzyme (20034198, Illumina)), then incubated at 55 °C for 10 min. The reaction was stopped by adding 0.4 μl 0.1% sodium dodecyle sulfate (Fisher Scientific, BP166-500). Indexing PCR reactions were performed by adding 0.4 μl of 5 μM i5 indexing primer (IDT), 0.4 μl of 5 μM i7 indexing primer (IDT), and 1.2 μl of KAPA HiFi Non-Hot Start Master Mix (Kapa Biosystems) using 12 amplification cycles. Libraries were purified using two purification rounds with a ratio of 0.8x and 0.7x AMPure beads. Library quantity and quality was assessed using a Bioanalyzer (Agilent) and Qubit. All steps were done manually using 8-strip PCR tubes and PCR reactions were carried out on a 96-plate thermal cycler (Biorad).
Libraries were pooled and sequenced on a Nextseq550 sequencer (Illumina) using single end 63bp for Read 1 and 12bp for index 1 with a high output 75bp kit (20024906, Illumina).

treatment_protocol: 18-month old mice were anesthetized with 2.5% isoflurane and then placed in a stereotactic instrument (KOPF). 3µl of a pool of young mouse CSF (as described above) or aCSF were injected to the right lateral ventricle using a digital pump (WPI syringe pump with Micro4t controller model UMP3T-1) at a pace of 1 µl/min. 1hr or 6hr following the injection, mice were perfused and contralateral hippocampus was dissected and used for RNAseq to avoid gene signatures induced by local immune response to the surgery. In labeled Fgf17 experiments, 10µg of mouse Fgf17 (7400-FG-025/CF, R&D) was conjugated to Alexa Fluor 647 using the lightning-link conjugation kit (ab269823, ThermoFisher) following the manufacturer’s instructions and then loaded twice on a 3kD MWCO Amicon Ultra centrifugal filters (UFC500396, ThermoFisher) and spun 30min 14,000g at 4 deg for free dye cleanup and buffer exchange with aCSF. As control, a parallel labeling reaction (dye only control) was carried with a similar volume of aCSF as input. In CSF labeling experiment, 1ml of human CSF was conjugated to Alexa Fluor 647 (ThermoFisher) using NHS chemistry and then loaded on a 3kD MWCO Amicon Ultra centrifugal filters (UFC500396,, ThermoFisher) and spun 30min 14,000g at 4 deg for free dye cleanup and buffer exchange with aCSF and for protein concentration. 0.5µg in 2µl of labeled Fgf17, dye-only control or YH-CSF were injected at a pace of 1 µl/min to young (2-3 months) mice and mice were taken down 2 or 3hr post-injection. Mice received post-surgical buprenorphine and Baytril.

tag: experiment batch

tag: experiment type

value: RNA-seq

value: Aged

tag: Sex

value: Male

tag: experimental group

value: Control

tag: timepoint

tag: specimen

value: Aged mouse CSF

value: Hippocampus

value: OPC

tag: cell compartment

value: Nucleus


title: Aged OPCs Artificial CSF 16hr sample 3

tag: age

value: Artificial CSF


title: XF 970_AltN171

value: splenic B cells

tag: genotype

value: WT

value: cytokine stimulation


title: lung single cell 263

description:
lung single cell 263
898s_K8

tag: tissue

value: lung

value: adult mice


title: Aged OPCs Aged CSF 16hr sample 3


title: lung single cell 262

description:
lung single cell 262
898s_K7


title: lung single cell 271

description:
lung single cell 271
898s_L16


title: Aged OPCs Artificial CSF 16hr sample 2


title: Aged OPCs Young CSF 16hr sample 4

value: Treatment

value: Young mouse CSF


title: lung single cell 260

description:
lung single cell 260
898s_K5


title: lung single cell 257

description:
lung single cell 257
898s_K2


title: lung single cell 259

description:
lung single cell 259
898s_K4


title: lung single cell 258

description:
lung single cell 258
898s_K3


title: lung single cell 313

description:
lung single cell 313
898s_N10


title: Aged OPCs Young CSF 16hr sample 2


title: Aged OPCs Aged CSF 16hr sample 1


title: Aged OPCs Aged CSF 16hr sample 2


title: Aged OPCs Young CSF 16hr sample 3


title: lung single cell 255

description:
lung single cell 255
898s_K23


title: Aged OPCs Young CSF 16hr sample 1


title: lung single cell 254

description:
lung single cell 254
898s_K22


title: lung single cell 261

description:
lung single cell 261
898s_K6


title: lung single cell 256

description:
lung single cell 256
898s_K24


title: Aged OLs Young CSF 6hr sample 4

source_name: Hippocampus

value: OL


title: lung single cell 253

description:
lung single cell 253
898s_K21


title: lung single cell 252

description:
lung single cell 252
898s_K20


title: lung single cell 249

description:
lung single cell 249
898s_K18


title: Aged OLs Young CSF 6hr sample 3

value: RNA-seq


title: lung single cell 245

description:
lung single cell 245
898s_K14


title: Aged OLs Artificial CSF 6hr sample 3

value: Aged


title: lung single cell 251

description:
lung single cell 251
898s_K1


title: lung single cell 246

description:
lung single cell 246
898s_K15


title: Aged OLs Young CSF 6hr sample 2

value: Male


title: lung single cell 250

description:
lung single cell 250
898s_K19


title: Aged OLs Young CSF 1hr sample 2


title: lung single cell 242

description:
lung single cell 242
898s_K11


title: Aged OLs Young CSF 6hr sample 1


title: Aged OLs Artificial CSF 6hr sample 4

value: Control


title: lung single cell 248

description:
lung single cell 248
898s_K17


title: lung single cell 240

description:
lung single cell 240
898s_J9


title: Aged OPCs Artificial CSF 16hr sample 1


title: Aged OLs Artificial CSF 6hr sample 1


title: Aged OLs Young CSF 1hr sample 4


title: lung single cell 247

description:
lung single cell 247
898s_K16


title: lung single cell 244

description:
lung single cell 244
898s_K13


title: Aged OLs Young CSF 1hr sample 1


title: Aged OLs Young CSF 1hr sample 3


title: lung single cell 241

description:
lung single cell 241
898s_K10


title: Aged OLs Artificial CSF 6hr sample 2


title: Aged OLs Artificial CSF 1hr sample 4


title: lung single cell 243

description:
lung single cell 243
898s_K12


title: lung single cell 237

description:
lung single cell 237
898s_J6


title: Aged OLs Artificial CSF 1hr sample 3


title: Aged OLs Artificial CSF 1hr sample 2


title: Aged OLs Artificial CSF 1hr sample 1


title: lung single cell 235

description:
lung single cell 235
898s_J4


title: lung single cell 239

description:
lung single cell 239
898s_J8


title: lung single cell 232

description:
lung single cell 232
898s_J24


title: Aged OPCs Young CSF 6hr sample 3


title: Aged OPCs Artificial CSF 6hr sample 4


title: lung single cell 236

description:
lung single cell 236
898s_J5


title: lung single cell 233

description:
lung single cell 233
898s_J2


title: Aged OPCs Young CSF 6hr sample 2


title: lung single cell 234

description:
lung single cell 234
898s_J3


title: lung single cell 231

description:
lung single cell 231
898s_J23


title: Aged OPCs Artificial CSF 6hr sample 3


title: Aged OPCs Young CSF 6hr sample 1


title: Aged OPCs Artificial CSF 6hr sample 2


title: lung single cell 238

description:
lung single cell 238
898s_J7


title: lung single cell 229

description:
lung single cell 229
898s_J21


title: lung single cell 230

description:
lung single cell 230
898s_J22


title: lung single cell 228

description:
lung single cell 228
898s_J20


title: Aged OPCs Artificial CSF 6hr sample 1


title: lung single cell 227

description:
lung single cell 227
898s_J1


title: Aged OPCs Young CSF 1hr sample 3


title: lung single cell 226

description:
lung single cell 226
898s_J19


title: Aged OPCs Young CSF 6hr sample 4


title: Aged OPCs Young CSF 1hr sample 2


title: Aged OPCs Young CSF 1hr sample 1


title: lung single cell 225

description:
lung single cell 225
898s_J18


title: Aged OPCs Artificial CSF 1hr sample 4


title: lung single cell 223

description:
lung single cell 223
898s_J16


title: Aged OPCs Artificial CSF 1hr sample 3


title: Aged OPCs Artificial CSF 1hr sample 1


title: Aged OPCs Young CSF 1hr sample 4


title: lung single cell 224

description:
lung single cell 224
898s_J17


title: lung single cell 221

description:
lung single cell 221
898s_J14


title: Aged OLs sample 2

growth_protocol: Young and aged C57BL6 mice.


title: Aged OLs sample 3


title: lung single cell 220

description:
lung single cell 220
898s_J13


title: lung single cell 218

description:
lung single cell 218
898s_J11


title: lung single cell 217

description:
lung single cell 217
898s_J10


title: Young OLs sample 4

value: Young


title: Young OLs sample 3

value: Hippocampus


title: lung single cell 216

description:
lung single cell 216
898s_I9


title: lung single cell 219

description:
lung single cell 219
898s_J12


title: lung single cell 215

description:
lung single cell 215
898s_I8


title: lung single cell 213

description:
lung single cell 213
898s_I6


title: lung single cell 214

description:
lung single cell 214
898s_I7


title: Aged OLs sample 1


title: Aged OPCs Artificial CSF 1hr sample 2

value: OPC


title: Aged OPCs sample 4

value: Nucleus


title: Young OLs sample 1


title: Aged OPCs sample 3


title: Young OLs sample 2


title: Young OPCs sample 4


title: lung single cell 212

description:
lung single cell 212
898s_I5


title: Aged OPCs sample 1


title: Young OPCs sample 3


title: lung single cell 222

description:
lung single cell 222
898s_J15


title: Aged OPCs sample 2


title: lung single cell 211

description:
lung single cell 211
898s_I4


title: lung single cell 207

description:
lung single cell 207
898s_I23


title: lung single cell 208

description:
lung single cell 208
898s_I24


title: lung single cell 209

description:
lung single cell 209
898s_I2


title: lung single cell 206

description:
lung single cell 206
898s_I22


title: Young OPCs sample 1


title: Young OPCs sample 2


title: ruxolitinib replicate 4

city: Portland

first: Sarah

middle: Ann

last: Carratt

state: Oregon

address: 3181 S.W. Sam Jackson Park Road, Mail Code KR-HEM

institute: OHSU

description: RNAseq

data_processing:
Sequencing from Bulk RNA seq was aligned using STAR
Differential Expression was determined using Deseq2
Genome_build: hg38 or mm10

source_name: CSF3RT618I+SETBP1D868N cell line

extract_protocol: Libraries were prepared by BGI

value: primary C57BL/6 mouse bone marrow cells immortalized by the retroviral overexpression of CSF3R and SETBP1

tag: treatment

value: 100 nM ruxolitinib

tag: time point

value: 24 hours

tag: antibody


title: A150_aCD40-TGF_Sg3_4

city: Toulouse

first: Chloé

last: Oudinet

address: 205 route de Narbonne

department: Oncology

institute: IPBS

data_processing:
Library strategy: CSR-HTGTS-Seq
Standard basecalling formats for Nextseq reads
Nextseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9_AJ851868ins reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: mm9_AJ851868ins
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

source_name: Splenic mature B cells

treatment_protocol: Primary splenic B cells were cultured in RPMI medium and stimulated with anti-CD40+IL4 or anti-CD40+TGFb for 96 hrs.

tag: activation

tag: treatment protocol

value: cytokine stimulation

tag: target locus

value: RPMI1640; 15percent FBS


title: lung single cell 205

description:
lung single cell 205
898s_I21

tag: strain

value: lung

value: adult mice


title: ruxolitinib replicate 2

description: RNAseq

tag: cell type


title: lung single cell 210

description:
lung single cell 210
898s_I3


title: ruxolitinib replicate 1

description: RNAseq


title: A150_aCD40-TGF_Sg3_2

tag: growth conditions


title: lung single cell 204

description:
lung single cell 204
898s_I20


title: A150_aCD40-TGF_Sg3_1


title: WT_aCD40-TGF_Sg3_3

value: WT


title: WT_aCD40-TGF_Sg3_2


title: A150_aCD40-TGF_Sµ_2


title: lung single cell 203

description:
lung single cell 203
898s_I1


title: WT_aCD40-TGF_Sg3_1


title: A150_aCD40-TGF_Sµ_3


title: lung single cell 303

description:
lung single cell 303
898s_M23


title: lung single cell 202

description:
lung single cell 202
898s_I19


title: A150_aCD40-TGF_Sµ_1


title: ruxolitinib replicate 3

description: RNAseq


title: A150_aCD40-TGF_Sg3_3


title: WT_aCD40-TGF_Sµ_2


title: lung single cell 201

description:
lung single cell 201
898s_I18


title: WT_aCD40-TGF_Sµ_3


title: lung single cell 200

description:
lung single cell 200
898s_I17


title: ORY1001 + ruxolitinib replicate 2

description: RNAseq

value: 30 nM ORY1001 + 100 nM ruxolitinib


title: A150_aCD40-IL4_Sg3_3


title: ORY1001 + ruxolitinib replicate 4

description: RNAseq


title: ORY1001 + ruxolitinib replicate 1

description: RNAseq


title: lung single cell 199

description:
lung single cell 199
898s_I16


title: A150_aCD40-IL4_Sg3_2


title: ORY1001 + ruxolitinib replicate 3

description: RNAseq


title: A150_aCD40-IL4_Sg3_1


title: ORY1001 replicate 4

description: RNAseq


title: WT_aCD40-IL4_Sg3_3


title: ORY1001 replicate 2

description: RNAseq


title: lung single cell 197

description:
lung single cell 197
898s_I14


title: A150_aCD40-IL4_Sµ_4


title: WT_aCD40-IL4_Sg3_2


title: ORY1001 replicate 3

description: RNAseq


title: lung single cell 198

description:
lung single cell 198
898s_I15


title: ORY1001 replicate 1

description: RNAseq


title: A150_aCD40-IL4_Sµ_3


title: WT_aCD40-IL4_Sg3_1


title: lung single cell 196

description:
lung single cell 196
898s_I13


title: A150_aCD40-IL4_Sµ_2


title: lung single cell 195

description:
lung single cell 195
898s_I12


title: A150_aCD40-IL4_Sµ_1


title: GSK2879552 + ruxolitinib replicate 4

description: RNAseq

value: 100 nM GSK2879552 + 100 nM ruxolitinib


title: WT_aCD40-IL4_Sµ_3


title: lung single cell 194

description:
lung single cell 194
898s_I11


title: Young CSF sample 7

description:
raw.counts.mean.samples.csv
YM-CSF_R7

extract_protocol:
Frozen dissected hippocampi were thawed on ice and homogenized in 350ml RLT buffer by 20 strokes using a manual homogenizer and total RNA was isolated with the RNeasy Plus Micro kit (Qiagen, 74034). RNA quantity and quality were assessed by Agilent 2100 Bioanalyzer (Agilent Technologies). All samples passed a quality-control threshold (RIN ≥ 9) to proceed to library preparation and RNA-seq on .
Done by Novogene: After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.
Done by Novogene: Hiseq 4000 (Illumina) using paired-end 100-bp reads. Libraries were sequenced to a depth of >20 million reads per sample

tag: experiment batch

tag: experiment type

value: RNA-seq

value: Aged

tag: Sex

value: Treatment

value: Young mouse CSF

value: Whole cell


title: lung single cell 193

description:
lung single cell 193
898s_I10


title: GSK2879552 + ruxolitinib replicate 3

description: RNAseq


title: lung single cell 192

description:
lung single cell 192
898s_H9


title: WT_aCD40-TGF_Sµ_1


title: Young CSF sample 3

description:
raw.counts.mean.samples.csv
YM-CSF_R3

value: Male

tag: experimental group

tag: timepoint

tag: specimen

value: Hippocampus


title: lung single cell 191

description:
lung single cell 191
898s_H8

tag: age

tag: genotype