title: Dye Control

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

description: Technical Dye Control

hyb_protocol: 1. Fluorescently labeled tRNAs were hybridized on the microarrays for 16 h at 60°C in a Hyb4 microarray hybridization system (Digilab) supplemented with polyA (0.17 mg/ml) and salmon sperm DNA (0.17 mg/ml). 2. Microarrays were washed once in 2× SSC/0.1% SDS (50°C), once in 1× SSC/0.1% SDS (42°C) and then three times in 0.1× SSC (42°C). 3. Arrays were dried and stored in the dark at 4°C.

scan_protocol: Arrays were scanned with a GenPIX 4200A (Molecular Devices) instrument.

data_processing:
1. TIF-files of scanned arrays were analyzed using the GenePix Pro 7 (Molecular Devices) software.
2. Ratios of  Cy3/Atto635 fluorescence signals were calculated for individual spots based on median fluorescence signal (background fluorescence subtraction).
3. Cy3 532/Atto635 ratios were normalized to Cy3 532/Atto635 values of tRNA standards (e.g. median Cy3 532/Atto635 ratios of the four tRNA standards) for individual blocks.
4. Normalized Cy3 532/Atto635 ratios for individual blocks were averaged, representing final Cy3 532/Atto635 ratios; detailed protocol for  normalization using the dye control slide is published in: https://www.protocols.io/view/microarray-based-quantification-of-cellular-trnas-hfcb3iw or in : Dittmar KA, Mobley EM, Radek AJ, Pan T. (2004) Exploring the regulation of tRNA distribution on the genomic scale. J Mol Biol 12, 31-47

organism: Escherichia coli BW25113

source_name: Escherichia coli BW25113_delta_hslR total lysate

label_protocol:
1. Equal amounts of in vitro synthesized tRNA standards (4 pmol each; human tRNAGln1, yeast tRNAPhe, human tRNAHis1, yeast tRNAAla) were added to 5 µg extracted total RNA.
2. Cy3 or Atto653 containing oligonucleotides (Microsynth) were ligated to tRNA 3'-CCA ends using 20 U/μl T4 DNA ligase (New England Biolabs) for 1h at RT in the presence of 15% DMSO (Sigma-Aldrich).

growth_protocol:
E. coli BW25113ΔhslR were transformed with N-terminal FLAG tagged pBAD-Hsp15 plasmids were grown overnight from single colony in LB supplemented with ampicillin.
Next day overnight cultures were diluted to starting OD600 of 0.05 in LB supplemented with ampicillin.

extract_protocol: For deacylation, lysate and immunoprecipitated samples were incubated with 190 mM Tris-HCl, pH = 9.0, 0.15 M EDTA, 0.75% (w/v) SDS at room temperature for 45 minutes, before neutralisation with an equal volume of 2 M NaOAc, pH = 5.5. RNA was extracted with 5:1 acidic phenol:chloroform, precipitated with ethanol, and resuspended in ddH2O.

treatment_protocol: Cells were grown with intensive shaking till OD600 of 0.5 and were induced with 0.00005% (v/v) arabinose and grown at 30° C until the O.D. reached 1.5. The cells were then heat shocked at 50° C for 20 minutes prior to harvesting by centrifugation

tag: strain

tag: genotype


title: EPEG_0.16_-S9_2

status: Public on Nov 15 2022

type: SRA

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

library_source: transcriptomic

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.20.0
Alignment was performed using STAR v2.7.8a
Gene counts were performed with qCount in the QuasR R package v1.30.0
Normalization was performed with DESeq2 v1.30.1
Assembly: Biospyder Human S1500+ v2.0
Supplementary files format and content: count_table.tsv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.
Library strategy: TempO-Seq

molecule: total RNA

organism: Homo sapiens

source_name: Spleen

growth_protocol: All experiments were performed with human lymphoblastoid TK6 (IVTG) cells (#13051501) purchased from Sigma-Aldrich (Oakville, ON). Cells were grown in RPMI1640 cell culture medium (ThermoFisher Scientific, Ottawa, ON) supplemented with 10% horse serum (ThermoFisher Scientific, Ottawa, ON), 2 mM L-Glutamine (ThermoFisher Scientific, Ottawa, ON), 1.8 mM sodium pyruvate (ThermoFisher Scientific, Ottawa, ON), and 100 U/mL of penicillin and streptomycin (ThermoFisher Scientific, Ottawa, ON). Cells were incubated at 37°C with 5% CO2 and maintained below 1x106/mL and >90% viability.

extract_protocol:
Cell lysates were used directly for TempO-Seq library building
The TempO-Seq® Human Surrogate+Tox Panel (S1500+) v2.0 (BioSpyder Technologies, Carlsbad, CA, USA) assay was completed following the manufacturer’s instructions in a 96-well plate format. Each 96-well plate included three assay controls in duplicate: a negative no-cell lysate (1X TempO-Seq® Enhanced Lysis buffer only), Human Reference Total RNA (Takara Bio, CA, USA), and Human Brain Reference Total RNA (Takara Bio, CA, USA). Briefly, for each treatment, 2 µL of cell lysate in 1X TempO-Seq® Enhanced Lysis buffer was hybridized to the Human S1500+ Surrogate detector oligo (DO) probe mix (V2.0), incubated at 70°C for 10 minutes, then ramped down to 45°C over 50 minutes (0.5°C/minute). A nuclease digestion followed to remove excess or incorrectly bound DOs at 37°C for 1 hour. The bound DO pairs were then ligated together at 37°C for 1 hour and 15 minutes at 80°C to generate templates for amplification. A 10 µL aliquot of amplification template was transferred to its respective well in the TempO-Seq® PCR Pre-Mix and Primers plate and amplified on the CFX96 thermocycler (Bio-Rad, Mississauga, ON, Canada) with the following program: 37°C for 10 min, 95°C for 1 min; 25 cycles of 95°C for 10 sec, 65°C for 30 sec, 68°C for 30 sec; 68°C for 2 min. For library building and purification, three 96-well plates (288 sample libraries) were pooled together (5 µL per sample) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Cleanup Kit (Clontech Laboratories Inc., Bethlehem, PA, USA) with the adjustments specified by the TempO-Seq® Assay User Guide. The pooled purified TempO-Seq® libraries were then diluted, quantified, and assessed for quality using the Agilent High Sensitivity D1000 TapeStation (Agilent Technologies, Santa Clara, CA, USA) and the qPCR KAPA Library Quantification Kit (Universal qPCR Master Mix) for Illumina NextSeq 500. Samples were sequenced on a total of two NextSeq® 500/550 High Output (75-cycle) flow cells using an Illumina NextSeq® 500 Sequencing Platform (Illumina, San Diego, CA, USA). A separate pool was completed for a fourth plate and an additional 96 sample libraries were added to the sequencing data for subsequent analysis.
The TempO-Seq® Human Surrogate+Tox Panel (S1500+) v2.0 - Index Sets F, G, H were used to index libraries (in two pools)

treatment_protocol: The cell density was adjusted to 1.5 x 105/mL, aliquoted in 96-well plates (100 µL/well), and exposed to 1% v/v solubilized test chemicals in DMSO in a six-point concentration range on a half-log distribution scale in duplicate. Six DMSO solvent controls were included per plate. For test chemicals requiring metabolic activation, the media were supplemented with 0.5% S9 Mix, Aroclor-1254 Induced Mutazyme® (Moltox, Boone, NC, USA). Treated cells were incubated at 37°C with 5% CO2 for 4H. Cells were collected via centrifugation at 300 x g for 5 minutes, washed with PBS, and resuspended in 1X TempO-Seq Enhanced Lysis buffer in PBS (40 µL/well) (BioSpyder Technologies, Carlsbad, CA, USA). If treated with 0.5% rat liver S9 fraction, cells were collected via centrifugation at 300 x g for 5 minutes, washed with PBS, resuspended in fresh media, and incubated at 37°C with 5% CO2 for a 3h recovery period. Following incubation, cells were collected, washed, and resuspended in 1X TempO-Seq® Enhanced Lysis buffer in PBS (40 µL/well) (BioSpyder Technologies, Carlsbad, CA, USA) and frozen at -80℃.

tag: tissue

value: Spleen

tag: cell line

tag: cell type

value: Lymphoblast

tag: chemical

value: EPEG

tag: chemical long_name

value: Etoposide

tag: dose

tag: treatment

tag: batch

value: Plate 3_IndexH

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: TGGAACGCT

tag: i5 index_id

value: GCACCTATT

tag: cas-rn


title: PBMCs from preeclampsia patient 4

city: Beijing

first: Juntao

last: Liu

address: No. 1, Shuaifu Garden, Dongcheng District

country: China

institute: Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences

description: Woman at 6 to 35 weeks postpartum

data_processing:
Raw reads of fastq files were derived from the raw BCL files using Illumina’s bcl2fastq converter.
Low-quality raw reads were removed in the presence of following quality assessment parameters: (i) the reads containing N of more than 3; (ii) more than 20% bases with quality value of ≤ 5; and (iii) the reads contained adapter sequence.
Alignment of reads to the GRCh38 genome was performed with STAR (14) included in CellRanger pipeline (version 3.1.0).
Genome_build:  GRCh38 for human data
Supplementary_files_format_and_content: The barcode, gene, expression matrix file of each sample

source_name: Peripheral blood

extract_protocol:
PBMCs were isolated from whole blood samples from each group using SepMate isolation tubes (StemCell Technologies, Cambridge, MA, USA).
Single-cell libraries were established using 10× Chromium single-cell 5’ library construction kit (10× Genomics, San Francisco, CA, USA) according to the manufacturer’s instructions.
The libraries were sequenced on the NovaSeq 6000 platform to generate 150 bp paired-end reads to an average depth of 30 million reads per cell.

tag: Sex

value: Female

tag: age

value: 32 years old

tag: blood pressure

value: PBMCs

tag: disease state

value: preeclampsia


title: E.coli IP/total tRNA 3-1

type: RNA

country: Germany

description: Biological replicate 3 of 3

tag: strain

tag: genotype

source_name: Escherichia coli BW25113_delta_hslR  IP


title: E.coli IP/total tRNA 2-1

description: Biological replicate 2 of 3


title: YZWJs24_2_P11

city: Kyoto

first: Masayoshi

last: Tsukahara

state: Kyoto

address: Shogoin kawahara-cho, sakyo-ku,

department: Research and Develpoment center

country: Japan

institute: CiRA foundation

description: SAMPLE 323

hyb_protocol: Gene expression hybridizatoin kits (Agilent) were used for hybridization.

scan_protocol: Slides were scanned on the SureScan microarray scanner system (Agilent).

data_processing: Fluorescent intensities were loaded and processed for backgroud correction by limma package of R software. Values were log-transformed and normalized by quantile normalization.

source_name: HLA homozygous iPSC

label_protocol: Low input quick amp labeling kits (Agilent) were used for cRNA labeling.

growth_protocol: Human iPSCs were maintained on iMatrix-511 (Nippi) coated plate with StemFit (AK03N, Ajinomoto).

extract_protocol: RNA was extracted by using TRIzol reagent (Thermo Fisher) and purifed by using RNA easy mini kit (QIAGEN).

treatment_protocol: Differentiation into three germ layers were conducted by using STEMDiff Trilineage differentiation kit (STEMCELL Technologies).

tag: cell type

value: iPSC

tag: gender

value: Male

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: Negative control_0_4

tag: tissue

tag: cell line

tag: chemical

value: (-) Lysis

tag: chemical long_name

value: Negative Control

tag: dose

tag: treatment

value: Negative control_0

tag: batch

value: Plate 2_IndexG

tag: sequencing pool

tag: technical control

value: T

tag: reference rna

value: TAGCTCTTC

value: GGTCTAGCT


title: YZWJs24_1_P11

description: SAMPLE 322


title: EPEG_0.16_-S9_1

value: Spleen

value: Lymphoblast

value: EPEG

value: Etoposide

value: Plate 3_IndexH

value: F

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: TGGAACGCT

tag: i5 index_id

value: GCCGTTACA

tag: cas-rn


title: E.coli IP/total tRNA 1-1

description: Biological replicate 1 of 3

tag: strain

tag: genotype


title: DMSO_0_12

tag: tissue

tag: cell line

tag: cell type

value: DMSO

value: Dimethyl sulfoxide

value: CGTAACTTA


title: YZWJs22_3_P11

description: SAMPLE 321

value: iPSC

tag: gender

value: Male

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: YZWJs22_2_P11

description: SAMPLE 320


title: YZWJs22_1_P11

description: SAMPLE 319


title: YZWJs21_3_P11

description: SAMPLE 318


title: YZWJs21_2_P11

description: SAMPLE 317


title: DMANN_1768_-S9_1

tag: chemical

value: DMANN

tag: chemical long_name

value: D-mannitol

tag: dose

tag: treatment

tag: batch

value: Plate 2_IndexG

tag: sequencing pool

value: TAGCTCTTC


title: NSACB18_1768_-S9_1

value: Spleen

value: Lymphoblast

tag: technical control

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: TCTAACCAT


title: NSACB18_1768_-S9_2

tag: tissue

tag: cell line

value: F

tag: i5 index_id

value: ATACGCAGC

tag: cas-rn


title: Negative control_0_3

tag: cell type

value: (-) Lysis

value: Negative Control

value: Negative control_0

value: T

value: GACTTCATT

value: GGTCTAGCT


title: DMSO_0_11

tag: chemical

value: DMSO

value: Dimethyl sulfoxide

value: CGTAACTTA


title: YZWJs20_3_P11

description: SAMPLE 315

value: iPSC

tag: gender

value: Male

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: DMANN_1768_-S9_2

value: Spleen

value: Lymphoblast

value: DMANN

tag: chemical long_name

value: D-mannitol

tag: dose

tag: treatment

tag: batch

value: Plate 2_IndexG

value: TAGCTCTTC

value: GCACCTATT


title: YZWJs21_1_P11

description: SAMPLE 316


title: YZWJs20_2_P12

description: SAMPLE 314


title: EPEG_0.11_-S9_1

value: EPEG

value: Etoposide

value: Plate 3_IndexH

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: solvent control

value: ATCGCGACT

value: GCCGTTACA


title: YZWJs20_1_P11

description: SAMPLE 313

value: iPSC


title: YZWJs19_3_P11

description: SAMPLE 312

value: Male


title: DMANN_2500_-S9_2

tag: tissue

tag: well

tag: i7 index_id

tag: index

value: GACTTCATT


title: DMANN_2500_-S9_1

tag: cell line

tag: cell type

tag: i5 index_id

tag: cas-rn


title: NSACB18_2500_-S9_2

tag: chemical

value: ATACGCAGC


title: NSACB18_2500_-S9_1

value: Spleen

tag: chemical long_name

value: TCTAACCAT


title: YZWJs19_2_P11

description: SAMPLE 311

tag: gender

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: YZWJs19_1_P11

description: SAMPLE 310


title: Brain_0_4

value: Lymphoblast

value: (+) Brain

value: Brain +ve control

tag: dose

tag: treatment

tag: batch

value: Plate 2_IndexG

tag: sequencing pool

value: T

value: TGCATGACA

value: GGTCTAGCT


title: YZWJs16_3_P11

description: SAMPLE 309


title: YZWJs16_1_P12

description: SAMPLE 307


title: YZWJs16_2_P11

description: SAMPLE 308


title: YZWJs15_3_P11

description: SAMPLE 306


title: DMSO_0_10

tag: tissue

value: DMSO

value: Dimethyl sulfoxide

tag: technical control

value: F

tag: reference rna

tag: solvent control

value: CGTAACTTA


title: YZWJs15_2_P11

description: SAMPLE 305

value: iPSC

value: Male


title: DMANN_3536_-S9_1

value: Spleen

tag: cell line

value: DMANN

value: D-mannitol

tag: well

tag: i7 index_id

tag: index

value: GCCGTTACA


title: NSACB18_3536_-S9_2

tag: cell type

value: Lymphoblast

tag: chemical

tag: i5 index_id

value: ATACGCAGC

tag: cas-rn


title: YZWJs15_1_P11

description: SAMPLE 304

tag: gender

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: YZWJs13_3_P11

description: SAMPLE 303


title: DMSO_0_9

tag: chemical long_name

tag: dose

tag: treatment

tag: batch

value: Plate 2_IndexG

value: T

value: TAAGGTAGC


title: NSACB18_3536_-S9_1

tag: tissue

tag: sequencing pool

tag: technical control

tag: reference rna

value: TGCATGACA

value: TCTAACCAT


title: Brain_0_3

tag: cell line

value: (+) Brain

value: Brain +ve control

tag: solvent control

value: F

tag: well

tag: i7 index_id

value: GGTCTAGCT


title: RWMH23_No23_3_P13

description: SAMPLE 284

tag: cell type

value: iPSC

value: Male

value: PBMC


title: DMANN_5000_-S9_1

value: Spleen

tag: chemical

value: DMANN

value: D-mannitol

tag: index

tag: i5 index_id

value: GCCGTTACA

tag: cas-rn


title: NSACB18_5000_-S9_2

value: Lymphoblast

tag: chemical long_name

value: ATACGCAGC


title: NSACB18_5000_-S9_1

tag: dose

value: Plate 2_IndexG


title: RWMH23_No23_1_P13

description: SAMPLE 282

tag: gender

tag: source cell

tag: generation method

value: pCE episomal vector


title: UHRR_0_4

tag: tissue

value: (+) UHRR

value: Universal human +ve control

tag: treatment

tag: batch

tag: sequencing pool

value: T

value: TCAGTACAT


title: DMANN_3536_-S9_2

tag: cell line

tag: technical control

value: F

tag: reference rna

tag: solvent control

value: TGCATGACA

value: GCACCTATT


title: RWMH23_No10_2_P13

description: SAMPLE 280

tag: cell type

value: iPSC

value: Male


title: DMANN_7071_-S9_2

value: Spleen

tag: chemical

tag: well

tag: i7 index_id

tag: index


title: RWMH23_No04_3_P13

description: SAMPLE 278

value: PBMC


title: RWMH23_No04_2_P13

description: SAMPLE 277


title: RWMH23_No04_1_P13

description: SAMPLE 276


title: YZWJs13_2_P11

description: SAMPLE 302

value: Cord blood


title: RWMH23_No03_3_P13

description: SAMPLE 275


title: DMANN_5000_-S9_2

value: DMANN

tag: chemical long_name

value: D-mannitol

tag: dose

value: TAAGGTAGC

tag: i5 index_id

tag: cas-rn


title: RWMH23_No03_2_P13

description: SAMPLE 274

tag: gender

tag: source cell

tag: generation method


title: NSACB18_7071_-S9_2

tag: tissue

value: Lymphoblast

tag: treatment

tag: batch

value: Plate 2_IndexG

tag: sequencing pool

value: ATACGCAGC


title: YZWJs13_1_P11

description: SAMPLE 301

value: pCE episomal vector


title: root, osspt5-1#12, rep2

city: nanjing

first: Jiajun

address: Weigang no.1, Xuanwu District, Nanjing City, Jiangsu Province

institute: Nanjing Agricultural University

data_processing:
The low-quality reads in the raw data were removed by the useful Perl script: (1) Trim Smart-seq2 public primer sequence from the Reads; (2) Remove the contaminated reads for adapters; (3) Remove the low quality reads; (4) Remove the reads whose N base more than 5% for total bases
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Assembly: IRGSP-1.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

organism: Oryza sativa

source_name: root

growth_protocol: Plant materials were cultivated in a growth chamber under a 15-h light /9-h darkness photoperiod (28°C/24°C) with 70% relative humidity.

extract_protocol:
RNA was harvested using pBIOZOL Plant Total RNA Extraction Reagent (BSC55M1). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA   Library Prep Kit for Illumina® (#E7530L, NEB, USA) following manufacturer's protocols.

value: root

tag: genotype


title: RWMH23_No23_2_P13

description: SAMPLE 283

tag: cell type


title: RWMH23_No02_3_P13

description: SAMPLE 272


title: root, WT, rep3

value: WT


title: NSACB18_7071_-S9_1

tag: cell line

tag: chemical

tag: technical control

value: F

tag: reference rna

tag: solvent control

value: TCAGTACAT

value: TCTAACCAT


title: RWMH23_No03_1_P13

description: SAMPLE 273

value: iPSC


title: DMSO_0_8

value: DMSO

tag: chemical long_name

value: Dimethyl sulfoxide

tag: dose

value: T

tag: well

tag: i7 index_id

tag: index

value: CGTAACTTA


title: RWMH23_No02_2_P13

description: SAMPLE 271

tag: gender

value: Male

tag: source cell

value: PBMC

tag: generation method


title: UHRR_0_3

tag: tissue

value: Spleen

value: (+) UHRR

value: Universal human +ve control

tag: treatment

tag: batch

value: ATTCGCTCT

tag: i5 index_id

value: GGTCTAGCT

tag: cas-rn


title: RWMH23_No10_3_P13

description: SAMPLE 281

tag: cell type

value: pCE episomal vector


title: RWMH23_No10_1_P13

description: SAMPLE 279


title: root, WT, rep1

value: root

tag: genotype

value: WT


title: root, osspt5-1#12, rep3


title: RWMH15_No10_3_P13

description: SAMPLE 269


title: shoot, osspt5-1#12, rep3

source_name: shoot

value: shoot


title: DMSO_0_7

tag: cell line

value: Lymphoblast

tag: chemical

value: Plate 2_IndexG

tag: sequencing pool

tag: technical control

value: F

tag: reference rna


title: DMANN_7071_-S9_1

value: DMANN

tag: chemical long_name

value: D-mannitol

tag: dose

tag: solvent control

tag: well

tag: i7 index_id

value: TCAGTACAT

value: GCCGTTACA


title: RWMH23_No02_1_P13

description: SAMPLE 270

value: iPSC

tag: gender

value: Male

tag: source cell

value: PBMC

tag: generation method


title: RWMH15_No10_1_P13

description: SAMPLE 267


title: RWMH15_No10_2_P13

description: SAMPLE 268


title: root, osspt5-1#12, rep1

tag: tissue


title: shoot, osspt5-1#12, rep2


title: RWMH15_No09_3_P13

description: SAMPLE 266


title: DMANN_10000_-S9_2

value: Spleen

tag: treatment

tag: batch

tag: index

tag: i5 index_id

value: GCACCTATT

tag: cas-rn


title: RWMH15_No09_2_P13

description: SAMPLE 265

tag: cell type


title: root, WT, rep2

tag: genotype


title: RWMH15_No09_1_P13

description: SAMPLE 264


title: RWMH15_No06_3_P13

description: SAMPLE 263


title: shoot, osspt5-1#12, rep1


title: NSACB18_10000_-S9_2

tag: cell line

tag: chemical

tag: sequencing pool

tag: technical control

tag: reference rna

value: ATTCGCTCT

value: ATACGCAGC


title: RWMH15_No06_2_P13

description: SAMPLE 262

value: pCE episomal vector


title: shoot, WT, rep3

value: WT


title: RWMH15_No05_3_P13

description: SAMPLE 260


title: RWMH15_No06_1_P13

description: SAMPLE 261


title: shoot, WT, rep2

value: shoot


title: NSACB18_10000_-S9_1

value: Lymphoblast

tag: chemical long_name

tag: dose

tag: solvent control

tag: well

tag: i7 index_id

value: TCTAACCAT


title: RWMH15_No05_2_P13

description: SAMPLE 259

tag: gender

tag: source cell

tag: generation method


title: NSACB14_417_-S9_2

tag: tissue

tag: treatment

tag: batch

value: Plate 2_IndexG

value: F

tag: index

value: ACTCATGTA

tag: i5 index_id

value: GGTCTAGCT


title: RWMH15_No05_1_P13

description: SAMPLE 258

tag: cell type


title: RWMH15_No04_3_P13

description: SAMPLE 257


title: shoot, WT, rep1

tag: genotype


title: NSACB14_417_-S9_1

tag: cell line

tag: chemical

tag: sequencing pool

tag: technical control

value: CGTAACTTA

tag: cas-rn


title: RWMH15_No04_2_P13

description: SAMPLE 256

value: iPSC


title: RWMH15_No04_1_P13

description: SAMPLE 255

value: Male


title: NSACB13_221_-S9_2

tag: chemical long_name

tag: dose

tag: reference rna

tag: solvent control

tag: well

value: ATACCGGCA


title: RWMH09_No11_3_P13

description: SAMPLE 254

tag: gender

tag: source cell

value: PBMC

tag: generation method


title: RWMH09_No11_2_P13

description: SAMPLE 253


title: NSACB13_221_-S9_1

tag: tissue

value: Spleen

tag: treatment

tag: batch

tag: i7 index_id

tag: index

value: GATTGTGTT


title: DMANN_10000_-S9_1

tag: cell line

tag: cell type

tag: chemical

value: DMANN

value: D-mannitol

value: ATTCGCTCT

tag: i5 index_id

value: GCCGTTACA


title: Ckit positive, scRNAseq

city: Amsterdam

first: micha

last: nethe

state: State

address: plesmanlaan 125

country: Netherlands

institute: Sanquin Bloedvoorziening

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Processing of data was performed using the Cell Ranger software v3.0.2. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: bone marrow

extract_protocol:
2500 mouse bone marrow E-cadherin+;cKIT+, Ecadherin+;cKIT- and LK cells were sorted and plated in duplicate in Methocult (Stemcell technologies, GF M3434). Colonies formed were characterized and counted 5-14 days after plating. E-cadherin+;cKIT+, Ecadherin+;cKIT- and LK cells were sorted and used at a 2x single cell suspension at final conc. 1000 cells/µl in 1xPBS containing 0.04% weight/volume BSA (400 µg/ml).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: Ckit positive

value: bone marrow

tag: strain

value: FVB


title: RWMH09_No11_1_P13

description: SAMPLE 252

value: pCE episomal vector


title: Ckit negative, scRNAseq

description: 10x Genomics

value: Ckit negative


title: RWMH09_No07_3_P13

description: SAMPLE 251


title: RWMH09_No07_2_P13

description: SAMPLE 250


title: NSACB12_6_-S9_1

value: Lymphoblast

tag: chemical long_name

tag: dose

value: Plate 2_IndexG

tag: sequencing pool

tag: technical control

value: F

value: ACTCATGTA

tag: cas-rn


title: RWMH09_No06_3_P13

description: SAMPLE 248

value: iPSC

tag: gender

value: Male

tag: source cell


title: RWMH09_No06_2_P13

description: SAMPLE 247

value: PBMC

tag: generation method


title: NSACB1_24_-S9_1

tag: tissue

value: Spleen

value: Methanone

tag: treatment

tag: reference rna

tag: solvent control

tag: well

value: TCTAACCAT


title: RWMH09_No04_3_P13

description: SAMPLE 245

tag: cell type


title: NSACB1_24_-S9_2

tag: cell line

tag: chemical

tag: batch

tag: i7 index_id

tag: index

value: ATACGCAGC


title: RWMH09_No04_2_P13

description: SAMPLE 244


title: RWMH09_No04_1_P13

description: SAMPLE 243


title: RWMH09_No02_3_P13

description: SAMPLE 242


title: NSACB14_589_-S9_1

tag: chemical long_name

tag: dose

tag: sequencing pool

value: GTTTATACT

tag: i5 index_id

value: CGTAACTTA


title: RWMH09_No02_2_P13

description: SAMPLE 241

tag: gender

tag: source cell


title: NSACB14_589_-S9_2

tag: tissue

tag: technical control

value: GGTCTAGCT

tag: cas-rn


title: RWMH09_No02_1_P13

description: SAMPLE 240

tag: generation method


title: NSACB13_313_-S9_2

tag: treatment

tag: reference rna

tag: solvent control

tag: well

value: ATACCGGCA


title: NSACB12_6_-S9_2

tag: cell line

tag: cell type

tag: chemical

tag: batch

value: GCACCTATT


title: RWMH29_P7

description: SAMPLE 238

value: pCE episomal vector


title: RWMH30_P7

description: SAMPLE 239


title: NSACB13_313_-S9_1

value: Lymphoblast

tag: chemical long_name

tag: dose

tag: i7 index_id

tag: index

value: GATTGTGTT


title: RWMH09_No07_1_P13

description: SAMPLE 249

tag: gender

tag: source cell


title: RWMH28_P7

description: SAMPLE 237


title: KO3

city: Phoenix

first: Min-Hyun

last: Kim

state: Arizona

address: 850 N. 5th St, Wexford 360H

department: College of Health Solutions

country: USA

institute: Arizona State University

description: Gene expression data from hypothalamus of ΔLepR mice

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on Mouse Gene ST 2.1 Strips, and were washed and stained using the Affymetrix Gene Atlas system (software version 2.0.0.460).

scan_protocol: Peg Arrays were scanned using the Affymetrix Gene Atlas system (software version 2.0.0.460).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Hypothalamus at 8 weeks old

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: Mice were housed on a 12-h light-dark cycle in the Unit for Laboratory Animal Medicine at the University of Michigan and fed ad libitum either a chow diet (9% fat in calories; TestDiet, St. Louis, MO)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Slugfl/fl mice were crossed with leptin receptor-CreERT2 mice to generate a leptin receptor-expressing cell-specific Slug knockout mouse model (ΔLepR). Mice were sacrificed at 8 weeks of age

tag: tissue

value: Hypothalamus

tag: genotype

value: Slugfl/fl;LepRCre/Cre (ΔLepR)

tag: age

value: 8 weeks old


title: RWMH09_No06_1_P13

description: SAMPLE 246

value: iPSC

value: Male

tag: generation method


title: RWMH27_P7

description: SAMPLE 236

value: PBMC


title: KO2


title: TLE - low freq 10

city: Tucson

first: Ryan

last: Sprissler

address: 1657 E Helen St

department: Center for Applied Genetics and Genomic Medicine

institute: University of Arizona

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.32
Trimmed sequence reads were mapped to GRCh37 using STAR version 2.5.2b
Read count extraction was performed using htseq-count version 0.6.1
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files

source_name: leukocyte

extract_protocol:
RNA was extracted using RNeasy lipid tissue mini kit (Qiagen, Valencia, CA) following manufacturer’s instructions
Libraries were constructed using a stranded mRNA-Seq Kit (TDS KR0960 – v3.15; KapaBiosystems, Wilmington, MA)

tag: disease

value: temporal lobe epilepsy

value: leukocyte

tag: seizure group

value: low

tag: baseline seizure_frequency


title: KO1


title: WT1

description: Gene expression data from hypothalamus of  Slugfl/fl mice

value: Slugfl/fl (Control)


title: WT2


title: RWMH26_P7

description: SAMPLE 235


title: RWMH25_P7

description: SAMPLE 234


title: TLE - low freq 9


title: RWMH24_P7

description: SAMPLE 233


title: NSACB12_9_-S9_1

value: Spleen

tag: cell line

tag: treatment

value: Plate 2_IndexG

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: solvent control

tag: well

value: GTTTATACT

tag: i5 index_id

value: GCCGTTACA

tag: cas-rn


title: WT3


title: TLE - high freq 5

tag: cell type

value: high


title: TLE - low freq 11


title: RWMH23_P7

description: SAMPLE 232

tag: gender

tag: source cell

value: pCE episomal vector


title: RWMH22_P7

description: SAMPLE 231


title: NSACB1_34_-S9_2

tag: tissue

value: Lymphoblast

tag: chemical

tag: chemical long_name

value: Methanone

tag: dose

tag: batch

tag: i7 index_id

tag: index

value: ATACGCAGC


title: TLE - high freq 4

tag: disease

tag: seizure group

tag: baseline seizure_frequency


title: RWMH20_P7

description: SAMPLE 229

value: iPSC

tag: generation method


title: RWMH21_P7

description: SAMPLE 230

value: Male


title: RWMH19_P7

description: SAMPLE 228

value: PBMC


title: RWMH18_P7

description: SAMPLE 227


title: NSACB14_833_-S9_2

tag: cell line

tag: treatment

tag: sequencing pool

tag: technical control

tag: reference rna

tag: solvent control

tag: well

value: GAACTGTAT

value: GGTCTAGCT


title: TLE - high freq 3

value: temporal lobe epilepsy

tag: cell type

value: leukocyte


title: TLE - low freq 7

value: low


title: TLE - low freq 8


title: RWMH17_P7

description: SAMPLE 226

tag: gender

tag: source cell


title: RWMH15_P7

description: SAMPLE 225


title: NSACB12_9_-S9_2

tag: tissue

value: Spleen

tag: chemical

tag: chemical long_name

tag: dose

tag: batch

value: Plate 2_IndexG

tag: i5 index_id

value: GCACCTATT

tag: cas-rn


title: RWMH13_P7

description: SAMPLE 223

tag: generation method


title: TLE - low freq 6

tag: disease

tag: seizure group

tag: baseline seizure_frequency


title: NSACB1_34_-S9_1

tag: cell line

tag: treatment

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: i7 index_id

tag: index

value: GTTTATACT

value: TCTAACCAT


title: RWMH11_P7

description: SAMPLE 222

tag: cell type

tag: gender

tag: source cell

value: pCE episomal vector


title: NSACB13_442_-S9_2

tag: tissue

value: Lymphoblast

tag: chemical

tag: chemical long_name

tag: dose

tag: batch

tag: solvent control

tag: well

value: ATACCGGCA


title: TLE - low freq 5

tag: disease

tag: seizure group

tag: baseline seizure_frequency


title: RWMH14_P7

description: SAMPLE 224

value: iPSC

tag: generation method


title: RWMH10_P7

description: SAMPLE 221

value: Male


title: RWMH09_P7

description: SAMPLE 220

value: PBMC


title: TLE - high freq 2

value: high


title: NSACB14_833_-S9_1

tag: cell line

tag: treatment

tag: sequencing pool

tag: technical control

tag: reference rna

value: GAACTGTAT

tag: i5 index_id

value: CGTAACTTA

tag: cas-rn


title: NSACB13_442_-S9_1

tag: tissue

tag: cell type

tag: chemical

tag: i7 index_id

tag: index

value: GATTGTGTT


title: RWMH08_P7

description: SAMPLE 219

tag: gender

tag: source cell


title: RWMH07_P7

description: SAMPLE 218


title: RWMH06_P7

description: SAMPLE 217


title: TLE - low freq 4

tag: disease

value: temporal lobe epilepsy

value: leukocyte

tag: seizure group

value: low


title: NSACB12_13_-S9_2

value: Spleen

tag: chemical long_name

tag: dose

tag: batch

value: Plate 2_IndexG

tag: solvent control

tag: well

value: GCACCTATT


title: RWMH05_P7

description: SAMPLE 216

tag: generation method


title: RWMH04_P7

description: SAMPLE 215


title: TLE - low freq 3

tag: baseline seizure_frequency


title: RWMH03_P7

description: SAMPLE 214


title: TLE - low freq 2


title: RWMH01_P7

description: SAMPLE 213


title: NSACB1_48_-S9_2

tag: cell line

value: Methanone

tag: treatment

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: i5 index_id

value: ATACGCAGC

tag: cas-rn


title: ILCLs31_3_P11

description: SAMPLE 170

tag: cell type

tag: gender

value: Female

tag: source cell

value: Cord blood

value: pCE episomal vector


title: TLE - low freq 1

tag: disease

tag: seizure group


title: NSACB1_48_-S9_1

tag: tissue

value: Lymphoblast

tag: chemical

tag: chemical long_name

tag: dose

tag: batch

tag: i7 index_id

tag: index

value: TCTAACCAT


title: NSACB14_1178_-S9_2

tag: cell line

tag: treatment

tag: sequencing pool

tag: solvent control

tag: well

value: GGGTTGTTA

value: GGTCTAGCT


title: RJWIs03_P11

description: SAMPLE 212

tag: cell type

value: iPSC

value: PBMC

tag: generation method


title: TLE - high freq 1

value: temporal lobe epilepsy

value: leukocyte

value: high

tag: baseline seizure_frequency


title: ILCLs31_2_P11

description: SAMPLE 169

tag: gender

tag: source cell


title: ILCLs31_1_P11

description: SAMPLE 168


title: ILCLs29_3_P11

description: SAMPLE 167


title: ILCLs29_2_P11

description: SAMPLE 166


title: MiaPaCa RMC4550 + LY3214996 3 weeks 2

first: Sara

last: Mainardi

address: Plesmanlaan 121

institute: The Netherlands Cancer Institute

data_processing:
Perform alignment against reference genome hg38 (BAM-files)
Default multiplexing - Index in separate read. Not barcoded
Assembly: hg38
Supplementary files format and content: csv file, matrix table with normalized abundance

source_name: subcutaneous tumor

extract_protocol:
RNA was extracted using the RNeasy Mini Kit from Qiagen and analyzed using an Agilent 2100 Bioanalyzer system
[W17] polyA+ stranded RNA Library prep from tissue

tag: tissue

value: subcutaneous tumor

value: Epithelial pancreatic cancer cells

tag: genotype

value: KRAS G12C


title: MiaPaCa RMC4550 + LY3214996 3 weeks 3


title: ILCLs29_1_P11

description: SAMPLE 165


title: NSACB12_13_-S9_1

value: Spleen

tag: chemical

tag: chemical long_name

value: Plate 2_IndexG

tag: technical control

value: F

tag: reference rna

value: GAACTGTAT

tag: i5 index_id

value: GCCGTTACA

tag: cas-rn


title: NSACB13_625_-S9_1

tag: cell line

value: Lymphoblast

tag: dose

tag: treatment

tag: batch

tag: i7 index_id

tag: index

value: GATTGTGTT


title: ILCLs28_3_P11

description: SAMPLE 164

tag: cell type

value: Female

value: Cord blood

tag: generation method

value: pCE episomal vector


title: ILCLs28_1_P11

description: SAMPLE 162

value: iPSC

tag: gender

tag: source cell


title: ILCLs28_2_P11

description: SAMPLE 163


title: MiaPaCa Vehicle 3 weeks 3

tag: tissue

tag: genotype

value: Vehicle


title: NSACB12_18_-S9_2

tag: chemical

tag: chemical long_name

tag: sequencing pool

tag: solvent control

tag: well

value: GGGTTGTTA

value: GCACCTATT


title: ILCLs27_3_P11

description: SAMPLE 161


title: NSACB12_18_-S9_1

tag: cell line

tag: technical control

tag: reference rna

tag: i5 index_id

tag: cas-rn


title: MiaPaCa Vehicle 3 weeks 2

value: subcutaneous tumor

tag: treatment


title: ILCLs27_2_P11

description: SAMPLE 160

tag: cell type


title: ILCLs27_1_P11

description: SAMPLE 159

tag: generation method


title: NSACB1_68_-S9_2

value: Methanone

tag: dose

tag: batch

tag: i7 index_id

tag: index

value: ATACGCAGC


title: NSACB14_1178_-S9_1

tag: tissue

value: Spleen

tag: chemical

value: CGTAACTTA


title: ILCLs23_3_P11

description: SAMPLE 158

tag: gender

tag: source cell


title: ILCLs23_2_P11

description: SAMPLE 157


title: MiaPaCa Vehicle 3 weeks 1

value: Epithelial pancreatic cancer cells

tag: genotype

value: KRAS G12C


title: ILCLs23_1_P11

description: SAMPLE 156


title: ILCLs21_3_P11

description: SAMPLE 155


title: ILCLs21_2_P11

description: SAMPLE 154


title: NSACB13_625_-S9_2

tag: cell line

tag: chemical long_name

value: Plate 2_IndexG

tag: sequencing pool

value: F

tag: solvent control

tag: well

value: ATACCGGCA


title: NSACB14_1666_-S9_2

value: Lymphoblast

tag: treatment

tag: technical control

tag: reference rna

value: AAGACTCTT

tag: i5 index_id

value: GGTCTAGCT

tag: cas-rn


title: NSACB1_68_-S9_1

tag: cell type

tag: dose

tag: batch

tag: i7 index_id

value: TCTAACCAT


title: ILCLs21_1_P11

description: SAMPLE 153

value: iPSC

tag: gender

value: Female

value: Cord blood

tag: generation method

value: pCE episomal vector


title: ILCLs20_3_P11

description: SAMPLE 152

tag: source cell


title: NSACB14_1666_-S9_1

tag: tissue

tag: cell line

tag: chemical

tag: index


title: MiaPaCa RMC4550 + LY3214996 3 weeks 1

value: subcutaneous tumor

tag: genotype


title: ILCLs20_2_P11

description: SAMPLE 151


title: CRISPR-screen_WT_1

city: Epalinges

first: Ping-Chih

last: Ho

address: Ch. des Boveresses 155

country: Switzerland

institute: Ludwig Cancer Institute, UNIL

library_source: genomic

data_processing:
The analysis pipeline and quality control were performed according to MAGeCK-VISPR algorithm with RRA function.
Assembly: Mouse metabolic library
Supplementary files format and content: raw reads count
Library strategy: CRISPR-screen

molecule: genomic DNA

source_name: Yumm1.7-Cas9 cell with metabolic gRNA pool transduction (engraft in WT mice)

growth_protocol: Mice were euthanized 15–18 days after tumor implantation and tumor genomic DNA was prepared from whole tumor tissue by salt precipitation method

extract_protocol:
Tumor tissues were homogenized in lysis Buffer containing proteinase K at 55°C overnight, and genomic DNA were extracted by isopropanol following removal of RNA and protein by RNase A and ammonium acetate.
16S amplificatoin by P5/P7 primer

tag: strain

value: melanoma

tag: host genotype

value: WT


title: NSACB13_884_-S9_2

value: Spleen

tag: chemical long_name

tag: treatment

tag: sequencing pool

tag: technical control

tag: reference rna

tag: solvent control

tag: well


title: ILCLs20_1_P11

description: SAMPLE 150

tag: cell type

tag: gender


title: ILCLs17_2_P11

description: SAMPLE 148

tag: source cell

tag: generation method


title: NSACB13_884_-S9_1

tag: tissue

tag: cell line

tag: dose

tag: batch

tag: i7 index_id

tag: i5 index_id

value: GATTGTGTT

tag: cas-rn


title: CRISPR-screen_Rag1KO_4

source_name: Yumm1.7-Cas9 cell with metabolic gRNA pool transduction (engraft in Rag1KO mice)

tag: strain

tag: host genotype


title: ILCLs17_3_P11

description: SAMPLE 149


title: CRISPR-screen_Rag1KO_3


title: ILCLs17_1_P11

description: SAMPLE 147


title: ILCLs16_3_P11

description: SAMPLE 146


title: NSACB12_25_-S9_2

tag: chemical

tag: chemical long_name

tag: treatment

tag: sequencing pool

tag: technical control

tag: index

value: GCACCTATT


title: CRISPR-screen_Rag1KO_2

tag: cell type


title: ILCLs16_2_P11

description: SAMPLE 145

tag: gender

tag: source cell

tag: generation method


title: ILCLs16_1_P11

description: SAMPLE 144


title: CRISPR-screen_WT_3

tag: cell line


title: ILCLs15_3_P11

description: SAMPLE 143


title: CRISPR-screen_WT_2


title: CRISPR-screen_Rag1KO_1


title: ILCLs15_2_P11

description: SAMPLE 142


title: NSACB1_95_-S9_2

tag: tissue

value: Methanone

tag: dose

tag: batch

value: Plate 2_IndexG

tag: reference rna

tag: solvent control

tag: well

value: ATACGCAGC


title: NSACB12_25_-S9_1

value: Lymphoblast

tag: chemical

value: F

tag: i7 index_id

tag: i5 index_id

value: GCCGTTACA

tag: cas-rn


title: ILCLs15_1_P11

description: SAMPLE 141


title: NSACB1_95_-S9_1

tag: chemical long_name

tag: treatment

tag: sequencing pool

tag: technical control

value: AAGACTCTT

value: TCTAACCAT


title: CRISPR-screen_Yumm1.7

source_name: Yumm1.7-Cas9 cell with metabolic gRNA pool transduction (in vitro)

tag: strain

tag: cell type

tag: host genotype


title: NSACB14_2356_-S9_2

tag: tissue

tag: cell line

tag: index

value: TCCTCAGCC

value: GGTCTAGCT


title: Primary cancer cell line from WT mice, WT4 (RNAseq)

data_processing:
Raw reads were trimmed using TrimGalore (v.0.6.6) according to quality from FastQC and adaptor.
The trimmed reads were mapped to the mm10 using STAR (v.2.7.9a).
The summarizeOverlaps function from the GenomicAlignments package (v.1.30.0) in R/Bioconductor (v.3.13) was used to define gene expression level by counting the alignments to exons
Assembly: mm10
Supplementary files format and content: normalized counts from DEseq2

source_name: Primary cancer cell line

growth_protocol: The primary tumors were chopped mechanicallyand digested with collagenase and dispase. The cell extract was disaggregated with trypsin and further cultured in DMEM with 10% getal bovine serum and !% penicillin-streptomycin.

extract_protocol:
RNA were collected by Qiagen RNeasy Kits
The sequencing library was prepared by illumine Truseq Stranded RNA kit

tag: genotype

value: primary tumor


title: ILCLs14_3_P11

description: SAMPLE 140

value: iPSC

tag: gender

value: Female

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: ILCLs14_2_P11

description: SAMPLE 139


title: NSACB14_2356_-S9_1

value: Spleen

tag: chemical

tag: dose

tag: batch

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

value: CGTAACTTA


title: Primary cancer cell line from WT mice, WT2 (RNAseq)

tag: strain

value: WT


title: NSACB13_1250_-S9_2

tag: cell type

tag: chemical long_name

tag: treatment

value: Plate 2_IndexG

tag: sequencing pool

tag: technical control

tag: i5 index_id

value: ATACCGGCA

tag: cas-rn


title: ΔBcFRQ1, LL, with nitrogen, rep 3

city: Valdivia

first: Javier

last: Canales

state: Los Ríos

address: Campus Isla Teja s/n

department: Instituto de Bioquimica y Microbiologia

country: Chile

institute: Universidad Austral de Chile

data_processing:
Sequenced reads were pseudo-aligned to the publicly available Botrytis cinerea B05.10 transcriptome obtained from Ensembl Fungi using kallisto (v0.46.2)
RNA-seq data was normalized using the R package DESeq2 package version 1.36.0
Assembly: ASM83294v1
Supplementary files format and content: Excel xlsx-file include raw-counts values for each sample and gene
Supplementary files format and content: Excel xlsx-file include normalized-counts values for each sample and gene

organism: Botrytis cinerea

source_name: whole fungus

growth_protocol: B05.10 and ΔBcFRQ1 strains of Botrytis cinerea were grown by 48 hours in CM media plates covered with celofan and depleted of nitrogen sources or complemented with glutamine 0.1M as nitrogen source.

extract_protocol:
RNA was harvested using Trizol and cleaned up with Qiagen RNAeasy Plant Minikit. 500 uL at 600ng/uL were send to Macrogen for the construction of sequencing libraries and sequencing.
RNA libraries for RNA-seq were prepared by TruSeq stranded mRNA library in Macrogen.

treatment_protocol: Plates were exposed to different ligth conditions during 48 hours. Constant Light (LL), Constant Darkness (DD) or Light Pulse (LP). For LP treatment plates were grown at DD during 44 hours and were exposed to light for 4 hours.

tag: tissue

value: whole fungus

value: Constant light, with nitrogen


title: ΔBcFRQ1, DD, with nitrogen, rep 3

value: Constant darkness, with nitrogen


title: B05.10, LL,  with nitrogen, rep 3


title: ΔBcFRQ1, LP, with nitrogen, rep 3

value: Light pulse, with nitrogen


title: ILCLs14_1_P11

description: SAMPLE 138

tag: gender

tag: source cell

tag: generation method


title: ILCLs13_3_P11

description: SAMPLE 137


title: B05.10, LP,  with nitrogen, rep 3


title: Primary cancer cell line from Rag1KO mice, KO7 (RNAseq)

tag: genotype


title: NSACB13_1250_-S9_1

tag: cell line

value: Lymphoblast

tag: chemical

tag: dose

tag: batch

value: F

tag: reference rna

tag: index

value: GATTGTGTT


title: Primary cancer cell line from Rag1KO mice, KO3 (RNAseq)

tag: strain

value: primary tumor


title: ILCLs13_2_P11

description: SAMPLE 136

tag: cell type

value: iPSC


title: B05.10, DD,  with nitrogen, rep 3

tag: treatment


title: NSACB12_35_-S9_2

tag: chemical long_name

tag: sequencing pool

tag: technical control

tag: solvent control

tag: well

tag: i7 index_id

value: TCCTCAGCC

value: GCACCTATT


title: ILCLs13_1_P11

description: SAMPLE 135

tag: gender

value: Female

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: Primary cancer cell line from Rag1KO mice, KO1 (RNAseq)

tag: genotype

tag: tissue


title: ΔBcFRQ1, LL, without nitrogen, rep 3

value: Constant light, without nitrogen


title: ΔBcFRQ1, LP, without nitrogen, rep 3

value: Light pulse, without nitrogen


title: ILCLs12_3_P11

description: SAMPLE 134


title: Primary cancer cell line from WT mice, WT6 (RNAseq)

value: WT


title: NSACB12_35_-S9_1

value: Spleen

tag: cell line

tag: chemical

tag: dose

tag: batch

value: Plate 2_IndexG

tag: i5 index_id

value: GCCGTTACA

tag: cas-rn


title: NSACB1_135_-S9_2

tag: cell type

tag: chemical long_name

value: Methanone

tag: treatment

tag: reference rna

tag: index

value: ATACGCAGC


title: Primary cancer cell line from WT mice, WT4 (ExomeSeq)

data_processing:
SNV/Indel calling, raw reads were converted to unmapped bam by using samtools, and the   unmapped bam files were marked duplicates with MarkDuplicatesSpark function from   GATK4 (v.4.2.3.0).
The processed bam files were mapped to the mouse reference genome   (mm10) by using BWA (v.0.7.17), and called variation by Mutect2 individually.
For calling copy number variations, the flat reference was first generated according to targets from Twist mouse exome panel.
The copy number variations were called by CNVkit with amplicon method and adjusted to b-allele with SNV/indel results from GATK4.
Assembly: mm10
Supplementary files format and content: vcf, cnr
Library strategy: Exome-seq

extract_protocol:
DNA were collected by Qiagen Blood & Cell Culture DNA Kits
The sequencing library was prepared by mouse exome panel (Twist Bioscicences, Cat. 102035)

tag: strain


title: ILCLs12_2_P11

description: SAMPLE 133

tag: gender


title: ΔBcFRQ1, DD, without nitrogen, rep 3

value: whole fungus

value: Constant darkness, without nitrogen


title: NSACB1_135_-S9_1

value: Lymphoblast

tag: sequencing pool

tag: technical control

value: F

tag: solvent control

tag: well

tag: i7 index_id

value: TCTAACCAT


title: Negative control_0_2

tag: tissue

tag: cell line

tag: chemical

value: (-) Lysis

value: Negative Control

value: Negative control_0

value: Plate 1_IndexF

value: T

value: GATAGCGGA

value: AAGTAGGCT


title: Primary cancer cell line from Rag1KO mice, KO7 (ExomeSeq)

tag: genotype

value: primary tumor


title: B05.10, LL,  without nitrogen, rep 3

value: Constant light, without nitrogen


title: B05.10, LP,  without nitrogen, rep 3

value: Light pulse, without nitrogen


title: DMBA_0.73_+S9_2

value: Spleen

value: DMBA

tag: dose

tag: batch

tag: i5 index_id

value: TTCCGAATT

tag: cas-rn


title: GLKVs31_3_P11

description: SAMPLE 131

tag: cell type

value: iPSC

value: Male

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: B05.10, DD,  without nitrogen, rep 3

value: whole fungus

tag: strain

tag: treatment

value: Constant darkness, without nitrogen


title: GLKVs31_2_P11

description: SAMPLE 130

tag: gender


title: ILCLs12_1_P11

description: SAMPLE 132

value: Female


title: Primary cancer cell line from Rag1KO mice, KO1 (ExomeSeq)


title: ΔBcFRQ1, LL, with nitrogen, rep 2

value: Constant light, with nitrogen


title: Primary cancer cell line from WT mice, WT6 (ExomeSeq)

value: WT


title: DMBA_0.73_+S9_1

value: Lymphoblast

tag: chemical long_name

value: Plate 1_IndexF

tag: sequencing pool

tag: technical control

value: F

tag: reference rna

tag: solvent control

tag: index

value: GATAGCGGA

value: AAACACCTT


title: GLKVs28_3_P11

description: SAMPLE 128


title: GLKVs31_1_P11

description: SAMPLE 129


title: ΔBcFRQ1, LP, with nitrogen, rep 2

tag: tissue

value: Light pulse, with nitrogen


title: Primary cancer cell line from WT mice, WT4 (ATAC-seq)

data_processing:
Conversion and demultiplexing: IlluminaBasecallsToMultiplexSam to generate one bam file per lane from the data on the Illumina machine, IlluminaSamDemux to demultiplex the bam file into multiple samples
Trimming: Sequencing adapters were removed and low-quality reads were filtered by fastp (0.20.1).
Alignment: Bowtie2 (version 2.4.1) with the ‘very-sensitive-local’ parameter, later duplicate reads were removed using samblaster (version 0.1.24).
Peak calling: Peaks were called using MACS2 (2.2.7.1) on each individual sample using the function callpeak with narrow peak setting.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
DNA were collected by Qiagen MinElute kit
50,000 cells were harvested and further processed with Illumina tagment DNA kit. Samples were purify with Qiagen MinElute kit with EB buffer.

tag: genotype

value: primary tumor


title: Primary cancer cell line from WT mice, WT6 (ATAC-seq)


title: ΔBcFRQ1, DD, with nitrogen, rep 2

value: Constant darkness, with nitrogen


title: NSACB8_884_+S9_1

value: Spleen

tag: cell line

tag: chemical

tag: dose

tag: batch

tag: well

tag: i7 index_id

value: GTGCATTAG


title: NSACB8_884_+S9_2

tag: cell type

tag: i5 index_id

value: ACAACCATC

tag: cas-rn


title: GLKVs28_2_P11

description: SAMPLE 127

value: iPSC

tag: gender

value: Male

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: GLKVs28_1_P11

description: SAMPLE 126


title: Primary cancer cell line from WT mice, WT2 (ATAC-seq)

tag: strain


title: B05.10, LL,  with nitrogen, rep 2

value: whole fungus

tag: treatment

value: Constant light, with nitrogen


title: Primary cancer cell line from WT mice, WT2 (ExomeSeq)

value: WT


title: Negative control_0_1

value: Lymphoblast

value: (-) Lysis

tag: chemical long_name

value: Negative Control

value: Negative control_0

value: Plate 1_IndexF

tag: sequencing pool

tag: technical control

value: T

tag: reference rna

tag: solvent control

tag: index

value: AGCCGATTA

value: AAGTAGGCT


title: Primary cancer cell line from Rag1KO mice, KO7 (ATAC-seq)

tag: genotype

tag: tissue

value: primary tumor


title: DMSO_0_6

value: Spleen

tag: cell line

tag: chemical

value: DMSO

value: Dimethyl sulfoxide

tag: dose

tag: batch

value: F

tag: well

tag: i7 index_id

value: GATAGCGGA

value: TAACGCGTC


title: Primary cancer cell line from Rag1KO mice, KO3 (ExomeSeq)


title: B05.10, LP,  with nitrogen, rep 2

value: whole fungus

value: Light pulse, with nitrogen


title: GLKVs27_3_P11

description: SAMPLE 125

tag: cell type

value: iPSC

tag: gender

value: Male

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: Primary cancer cell line from Rag1KO mice, KO3 (ATAC-seq)

tag: strain


title: DMSO_0_5

value: Lymphoblast

tag: chemical long_name

tag: treatment

value: Plate 1_IndexF

tag: sequencing pool

tag: technical control

tag: i5 index_id

tag: cas-rn


title: GLKVs27_2_P11

description: SAMPLE 124


title: DMBA_1.04_+S9_2

tag: tissue

tag: cell line

value: DMBA

tag: reference rna

tag: solvent control

tag: index

value: AGCCGATTA

value: TTCCGAATT


title: Primary cancer cell line from Rag1KO mice, KO1 (ATAC-seq)

tag: genotype

value: primary tumor


title: B05.10, DD,  with nitrogen, rep 2

value: Constant darkness, with nitrogen


title: DMBA_1.04_+S9_1

value: Spleen

tag: cell type

tag: chemical

tag: dose

tag: batch

tag: well

tag: i7 index_id

value: AAACACCTT


title: ΔBcFRQ1, LL, without nitrogen, rep 2

tag: strain

tag: treatment

value: Constant light, without nitrogen


title: ΔBcFRQ1, LP, without nitrogen, rep 2

value: Light pulse, without nitrogen


title: GLKVs27_1_P11

description: SAMPLE 123

tag: gender

tag: source cell

tag: generation method


title: NSACB8_1250_+S9_2

tag: tissue

tag: chemical long_name

tag: sequencing pool

tag: technical control

value: F

tag: i5 index_id

value: ACAACCATC

tag: cas-rn


title: GLKVs25_3_P11

description: SAMPLE 122

tag: cell type

value: iPSC


title: brain, N3AD6f

city: Trondheim

first: Katja

last: Scheffler

address: Edvard Griegs Gate 8

department: Department of Neuromedicine and Movement Sciences

country: Norway

institute: Norwegian University of Science and Technology

data_processing:
Unpaired reads were trimmed and filtered for quality. Quality of the trimmed reads were assessed using FastQC (v0.11.9) and FastQ-Screen (v.0.14.1). and reads per gene were counted using the Rsubread package in R (3.6.3). Differential expression was analyzed using the exact test method in EdgeR (3.32.1).
Reads were mapped using Hisat2
Reads per gene were counted using the Rsubread package in R (3.6.3).
Differential expression was analyzed using the exact test method in EdgeR (3.32.1).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of raw counts generated from Rsubread

source_name: brain

extract_protocol:
Total RNA was isolated from homogenized mouse brain using Allprep DNA/RNA/Protein kit  (Qiagen) according to the manufacturer’s instructions. RNA quality and concentration were measured using a RNA Pico chip on an Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: brain

tag: age

value: 6 month

tag: Sex

value: female


title: ΔBcFRQ1, DD, without nitrogen, rep 2

value: whole fungus

value: Constant darkness, without nitrogen


title: GLKVs25_2_P11

description: SAMPLE 121

value: Male

value: Cord blood

value: pCE episomal vector


title: NSACB8_1250_+S9_1

tag: cell line

value: Lymphoblast

tag: chemical

tag: dose

tag: batch

value: Plate 1_IndexF

tag: reference rna

tag: solvent control

tag: well

tag: index

value: AGCCGATTA

value: GTGCATTAG


title: B05.10, LL,  without nitrogen, rep 2

tag: tissue

tag: strain

tag: treatment

value: Constant light, without nitrogen


title: Brain_0_2

value: Spleen

value: (+) Brain

tag: chemical long_name

value: Brain +ve control

tag: sequencing pool

tag: technical control

value: T

tag: i7 index_id

value: ACCTGAGGC

tag: i5 index_id

value: AAGTAGGCT


title: GLKVs25_1_P11

description: SAMPLE 120

tag: cell type

value: iPSC

tag: gender

tag: source cell

tag: generation method


title: brain, AD6f

tag: genotype

value: brain

tag: age

value: 6 month

tag: Sex

value: female


title: brain, AD6m

value: male


title: B05.10, LP,  without nitrogen, rep 2

value: whole fungus

value: Light pulse, without nitrogen


title: DMSO_0_4

tag: cell line

value: Lymphoblast

tag: chemical

value: DMSO

value: Dimethyl sulfoxide

tag: dose

tag: batch

value: Plate 1_IndexF

value: F

tag: reference rna

tag: solvent control

tag: well

value: TAACGCGTC

tag: cas-rn


title: GLKVs19_3_P11

description: SAMPLE 119

value: Male

value: Cord blood

value: pCE episomal vector


title: GLKVs19_2_P11

description: SAMPLE 118


title: brain, N3AD1f

tag: strain

tag: tissue

value: 1 month


title: B05.10, DD,  without nitrogen, rep 2

tag: treatment

value: Constant darkness, without nitrogen


title: DMBA_1.46_+S9_2

value: Spleen

tag: cell type

value: DMBA

tag: chemical long_name

tag: sequencing pool

tag: technical control

tag: i7 index_id

tag: index

value: ACCTGAGGC

tag: i5 index_id

value: TTCCGAATT


title: brain, N3AD1m

tag: genotype

value: brain

tag: age

tag: Sex

value: male


title: DMBA_1.46_+S9_1

tag: cell line

value: Lymphoblast

tag: chemical

tag: dose

tag: batch

tag: reference rna

value: AAACACCTT


title: ΔBcFRQ1, LL, with nitrogen, rep 1

tag: tissue

value: whole fungus

tag: strain

value: Constant light, with nitrogen


title: ΔBcFRQ1, LP, with nitrogen, rep 1

tag: treatment

value: Light pulse, with nitrogen


title: GLKVs16_3_P11

description: SAMPLE 116

tag: cell type

value: iPSC

tag: gender

tag: source cell

tag: generation method


title: brain, AD1m


title: brain, AD1f

value: female


title: NSACB8_1768_+S9_2

tag: chemical long_name

value: Plate 1_IndexF

tag: sequencing pool

tag: technical control

value: F

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: ACAACCATC

tag: cas-rn


title: ΔBcFRQ1, DD, with nitrogen, rep 1

value: Constant darkness, with nitrogen


title: brain, N3AD6m

tag: genotype

tag: age

value: 6 month

tag: Sex


title: GLKVs16_2_P11

description: SAMPLE 115

value: Male

value: Cord blood

value: pCE episomal vector


title: NSACB8_1768_+S9_1

tag: tissue

value: Spleen

tag: cell line

tag: chemical

tag: dose

tag: batch

tag: reference rna

value: ACCTGAGGC

tag: i5 index_id

value: GTGCATTAG


title: GLKVs16_1_P11

description: SAMPLE 114

tag: cell type

tag: gender

tag: source cell

tag: generation method


title: Brain_0_1

value: Lymphoblast

value: (+) Brain

tag: chemical long_name

value: Brain +ve control

tag: treatment

tag: sequencing pool

tag: technical control

value: T

tag: solvent control

tag: well

tag: i7 index_id

value: TAGCGACAA

value: AAGTAGGCT


title: TD4

city: Vienna

first: Hana

last: Imrichova

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM, Vienna

data_processing:
conversion and demultiplexing: Base calling was performed by Illumina Real Time Analysis (v2.7.7) software and the base calls were converted to short reads using the IlluminaBasecallsToSam tool from the Picard toolkit (v2.19.2).
trimming and filtering: Sequencing adapters were removed, and the low-quality reads were filtered using the fastp software (v 0.20.1).
alignment: The short reads were aligned to the mm10/GRCm38 assembly of the mouse reference genome using Bowtie2 (v2.4.1) with the “-very-sensitive” parameter. PCR duplicates were marked using samblaster (v0.1.24), and the reads mapped to the ENCODE black-listed regions were discarded prior to peak calling.
bigWig generation: BigWig files were generated using the computeMatrix from the deepTools (v3.5.0), using the following parameters: -p max --binSize 10  --normalizeUsing RPGC --effectiveGenomeSize 2407883318 --extendReads 175.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: bigWig

source_name: murine melanoma tumor cells (EGFP+)

growth_protocol: The murine melanoma was induced in mTmG, BRafCA, PtenloxP, Tyr::CreERT2 mice with tamoxifen.

extract_protocol:
The tumors were digested by collagenase and dispase, and CD45+ cells were be removed before sorting. Live tumor cells with EGFP+ were sorted for ATAC-seq library preparation.
Illumina Tagment DNA Enzyme and Buffer Small Kit was used for library preparation with 1% Digitonin and Proteinase inhibitor cocktail.

treatment_protocol: Anti-CD4 and Anti-CD8 antibody were used for T cell depletion. T cell depletion was started from week 2 to week 5 after tamoxifen induction.

tag: strain

value: melanoma tumor cells

value: treated with anti-CD4/8 (T cell depletion)


title: TD3


title: GLKVs15_2_P11

description: SAMPLE 112

value: iPSC


title: B05.10, LP,  with nitrogen, rep 1

tag: tissue

value: whole fungus

value: Light pulse, with nitrogen


title: B05.10, LL,  with nitrogen, rep 1

value: Constant light, with nitrogen


title: DMSO_0_3

source_name: Spleen

tag: cell line

tag: chemical

value: DMSO

value: Dimethyl sulfoxide

tag: dose

value: Plate 1_IndexF

value: F

tag: index

value: TAACGCGTC

tag: cas-rn


title: TD2

tag: cell type


title: GLKVs15_1_P11

description: SAMPLE 111

tag: gender

value: Male

tag: source cell

value: Cord blood

value: pCE episomal vector


title: TD1


title: GLKVs19_1_P11

description: SAMPLE 117

tag: generation method


title: DMBA_2.07_+S9_1

value: Spleen

value: Lymphoblast

value: DMBA

tag: chemical long_name

tag: treatment

tag: batch

tag: reference rna

tag: i5 index_id

value: AAACACCTT


title: ΔBcFRQ1, LP, without nitrogen, rep 1

value: Light pulse, without nitrogen


title: NSACB8_2500_+S9_2

tag: sequencing pool

tag: technical control

tag: solvent control

tag: well

tag: i7 index_id

value: TAGCGACAA

value: ACAACCATC


title: C4

tag: strain

value: melanoma tumor cells

value: untreated


title: C3


title: TD5

value: treated with anti-CD4/8 (T cell depletion)


title: NSACB8_2500_+S9_1

tag: tissue

tag: cell line

tag: chemical

tag: dose

tag: index

value: GTGCATTAG


title: GLKVs13_2_P11

description: SAMPLE 109

tag: cell type

value: iPSC

tag: gender

tag: source cell

tag: generation method


title: GLKVs13_1_P11

description: SAMPLE 108


title: B05.10, LL,  without nitrogen, rep 1

value: whole fungus

tag: treatment

value: Constant light, without nitrogen


title: UHRR_0_2

value: (+) UHRR

tag: chemical long_name

value: Universal human +ve control

tag: batch

value: Plate 1_IndexF

value: T

tag: reference rna

value: F

value: GCTATCGAT

tag: i5 index_id

value: AAGTAGGCT

tag: cas-rn


title: GLKVs15_3_P11

description: SAMPLE 113

value: Male

value: Cord blood

value: pCE episomal vector


title: C2

value: melanoma tumor cells


title: B05.10, LP,  without nitrogen, rep 1

value: Light pulse, without nitrogen


title: DMSO_0_2

value: Spleen

value: Lymphoblast

value: DMSO

value: Dimethyl sulfoxide

tag: sequencing pool

tag: technical control

tag: solvent control

tag: well

tag: i7 index_id

value: TAACGCGTC


title: B05.10, DD,  with nitrogen, rep 1

tag: tissue

value: whole fungus

tag: strain

value: Constant darkness, with nitrogen


title: DMBA_2.07_+S9_2

tag: cell line

tag: cell type

tag: chemical

value: DMBA

tag: dose

value: Plate 1_IndexF

tag: index

value: TAGCGACAA

value: TTCCGAATT


title: ΔBcFRQ1, LL, without nitrogen, rep 1

tag: treatment

value: Constant light, without nitrogen


title: C1

value: untreated


title: B05.10, DD,  without nitrogen, rep 1

value: Constant darkness, without nitrogen


title: GLKVs10_2_P11

description: SAMPLE 106

value: iPSC

tag: gender

value: Male

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: DMBA_2.93_+S9_2

value: Spleen

value: Lymphoblast

tag: chemical long_name

tag: batch

value: F

tag: reference rna

value: GCTATCGAT

tag: i5 index_id

tag: cas-rn


title: DMBA_2.93_+S9_1

tag: sequencing pool

tag: technical control

tag: solvent control

tag: well

tag: i7 index_id

value: AAACACCTT


title: GLKVs10_1_P11

description: SAMPLE 105

tag: cell type


title: GLKVs13_3_P11

description: SAMPLE 110


title: NSACB8_3536_+S9_2

tag: tissue

tag: cell line

tag: chemical

tag: dose

value: ACAACCATC


title: ΔBcFRQ1, DD, without nitrogen, rep 1

value: whole fungus

tag: strain

tag: treatment


title: CT_rep1

first: Yi

last: Zuo

address: No. 50 Road Zhanghua

institute: Beijing Academy of Agriculture and Forestry Science

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed using fastp（version:0.20.1）, then mapped to 970103 V2 using moabs（version:1.3.2）.
The methylation level were normalized as  percentage using moabs (version:1.3.2)
Genome_build: CuGenDB 97103-v2 watermelon
Supplementary_files_format_and_content: bigWig files include DNA methlated values for each Sample

organism: Citrullus lanatus

source_name: flesh

extract_protocol:
Genomic DNA was extracted from fruits using a DNeasy Plant Maxi Kit (Qiagen).
Samples was used for library construction using Illumina’s standard DNA methylation analysis protocol and the New England Biolabs Ultra II DNA Library Prep Kit.

value: flesh

tag: age

value: 20 DAP

tag: genotype


title: BW_rep3

value: 10 DAP


title: GLKVs09_3_P11

description: SAMPLE 104

tag: gender

tag: source cell

tag: generation method


title: GLKVs09_2_P11

description: SAMPLE 103


title: NSACB8_3536_+S9_1

tag: chemical long_name

tag: batch

value: Plate 1_IndexF

tag: sequencing pool

tag: reference rna

tag: index

tag: i5 index_id

value: GTGCATTAG

tag: cas-rn


title: BW_rep1

tag: tissue


title: GLKVs09_1_P11

description: SAMPLE 102

tag: cell type


title: GLKVs10_3_P11

description: SAMPLE 107


title: SW_rep3

value: 5 DAP


title: GLKVs03_3_P11

description: SAMPLE 101

value: iPSC


title: SW_rep2


title: DMBA_4.14_+S9_2

tag: cell line

tag: chemical

value: DMBA

tag: dose

tag: technical control

tag: solvent control

tag: well

tag: i7 index_id

value: ATTGGTTGC

value: TTCCGAATT


title: GLKVs03_2_P11

description: SAMPLE 100

tag: gender

value: Male

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: GLKVs03_1_P11

description: SAMPLE 99


title: DMBA_4.14_+S9_1

value: Spleen

value: Lymphoblast

tag: chemical long_name

tag: treatment

tag: batch

tag: sequencing pool

value: F


title: SW_rep1

tag: age

tag: genotype


title: GLKVs02_3_P11

description: SAMPLE 98

tag: cell type


title: AP_rep3

tag: tissue

value: 1 DAP


title: NSACB8_5000_+S9_2

tag: cell line

tag: chemical

tag: reference rna

tag: index

tag: i5 index_id

value: ACAACCATC

tag: cas-rn


title: BW_rep2

value: flesh


title: AP_rep2


title: NSACB8_5000_+S9_1

tag: dose

tag: technical control

tag: solvent control

tag: well

tag: i7 index_id


title: GLKVs02_2_P11

description: SAMPLE 97

tag: gender

tag: source cell

tag: generation method


title: DMSO_0_1

value: DMSO

tag: chemical long_name

value: Dimethyl sulfoxide

tag: treatment

tag: batch

tag: sequencing pool

value: T

value: TAACGCGTC


title: NSACB5_884_+S9_2

tag: tissue

tag: cell line

tag: cell type

tag: chemical

value: Plate 1_IndexF

value: TGATTAAGC

value: AAGTAGGCT


title: GLKVs02_1_P11

description: SAMPLE 96

value: iPSC


title: AP_rep1

tag: age

tag: genotype


title: PD_rep3

value: 0 DAP


title: UHRR_0_1

value: (+) UHRR

value: Universal human +ve control

tag: dose

tag: technical control

tag: reference rna

tag: index

value: ATTGGTTGC

tag: i5 index_id

tag: cas-rn


title: GFP-TIS11B_transfection_rep3

city: New York

first: Christine

last: Mayr

state: NY

address: 417 E 68th Street

department: Cancer Biology and Genetics

institute: MSKCC

data_processing:
Raw fastq files were demultiplexed using the iCount python package (https://icount.readthedocs.io)
5’ and 3’ adapters were trimmed by Cutadapt
Trimmed reads were mapped to human genome (hg38) using STAR, and reads mapped to tRNA/rRNA were discarded.
Crosslink sites were called from bam files using the “xlsites” function of iCount, and peaks were finally called by aggregating crosslink sites using Paraclu.
All analysis was carried out on the iMaps platform (https://imaps.genialis.com/iclip).
Assembly: hg38
Supplementary files format and content: BED format; Peaks called by the iMaps platform.

growth_protocol: HEK293T cells were plated in six 10 cm dishes at 80% confluency in antibiotic free media

extract_protocol:
Cells were rinsed once with ice cold PBS and 6 mL of PBS was added to each plate before crosslinking. Cells were then irradiating once with 150mJ/cm2 in a Spectroline UV Crosslinker at 254nm. Irradiated cells were scraped into Eppendorf tubes, spun at 500g for 1 minute, and snap frozen. Crosslinked cell pellets were lysed in iCLIP lysis buffer (50mM Tris-HCl pH7.4, 100mM NaCl, 1% Igepal CA-630 (Sigma I8896), 0.1% SDS, 0.5% sodium deoxycholate), sonicated with the Bioruptor Pico for 10 cycles 30 seconds ON/30 seconds OFF, and supplemented with 0.5U of RNase I per 1mg/ml lysate for RNA fragmentation. Lysates were pre-cleared by centrifugation at 21,000xG at 4oC. A mix of Protein A/G Dynabeads (50ul of each per sample, Life Technologies) were coupled to 10ug of rabbit anti-GFP antibody (Abcam ab290). TIS11B protein-RNA complexes were immunoprecipitated from 1ml of crosslinked lysate and washed with high salt and PNK buffer. RNA was repaired by 3’ dephosphorylation and ligated to L3-IR adaptor (Zarnegar et al. 2016) on beads. Excess adaptor was removed by incubation with 5’ deadenylase and RecJf. TIS11B protein-RNA complexes were eluted from the beads by heating at 70oC for 1 minute. The complexes were then visualized via the infrared-labelled adaptor, purified with SDS-PAGE, and transfer to nitrocellulose membrane.
cDNA was synthesized with Superscript IV Reverse Transcriptase (Life Technologies) and circularized by CircLigase II. Circularized cDNA was purified with AmPURE bead-based purification (A63880, Beckman Coulter) and amplified by PCR.

treatment_protocol: 24 hours after seeding, cells were transfected by calcium phosphate with either 3ug GFP-TIS11B or 3 ug GFP per plate

value: WT

value: CaPO4 transfection with GFP-TIS11B

tag: rip antibody

value: anti-GFP antibody (Abcam ab290)

tag: assay

value: iCLIP-seq


title: GLKVs01_3_P11

description: SAMPLE 95

tag: gender

value: Male

tag: source cell

value: Cord blood

tag: generation method

value: pCE episomal vector


title: CD3+ T cells, NECA-negative, biological rep2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Human CD3+ T cells activated and cultured without 5'-N-ethylcarboxamidoadenosine (NECA) for three days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: PBMCs were isolated from the blood of healthy human volunteers by density gradient centrifugation on Ficoll-Paque (GE Healthcare, Upssala, Sweden), from which total CD3+ T cells were purified using the Pan T cell Isolation Kit human (Miltenyi Biotec, Bergisch Gladbach, Germany). T cells were cultured in TexMACS Medium research grade (Miltenyi Biotec, Bergisch Gladbach, Germany) for three days and stimulated with 0.75 μl/ml anti-CD3/anti-CD28 streptamer premix (iba Lifesciences, Göttingen, Germany)μl/ml anti-CD3/anti-CD28 streptamer premix (iba Lifesciences, Göttingen, Germany).

extract_protocol: Total RNA was prepared using TRIzol reagent (ambion, Life technologies, Carlsbad, USA), after which RNA quality was confirmed by capillary electrophoresis on an Agilent 2100 bioanalyzer.

treatment_protocol: To half of the cells from one donor, NECA (Sigma-Aldrich, St. Louis, USA) was added at a concentration of 50 μM (Positive), while the other half received the treatment described above (Negative).

value: CD3+ T cells

tag: treatment

value: Negative


title: NSACB5_884_+S9_1

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.20.0
Alignment was performed using STAR v2.7.8a
Gene counts were performed with qCount in the QuasR R package v1.30.0
Normalization was performed with DESeq2 v1.30.1
Assembly: Biospyder Human S1500+ v2.0
Supplementary files format and content: count_table.tsv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.
Library strategy: TempO-Seq

extract_protocol:
Cell lysates were used directly for TempO-Seq library building
The TempO-Seq® Human Surrogate+Tox Panel (S1500+) v2.0 (BioSpyder Technologies, Carlsbad, CA, USA) assay was completed following the manufacturer’s instructions in a 96-well plate format. Each 96-well plate included three assay controls in duplicate: a negative no-cell lysate (1X TempO-Seq® Enhanced Lysis buffer only), Human Reference Total RNA (Takara Bio, CA, USA), and Human Brain Reference Total RNA (Takara Bio, CA, USA). Briefly, for each treatment, 2 µL of cell lysate in 1X TempO-Seq® Enhanced Lysis buffer was hybridized to the Human S1500+ Surrogate detector oligo (DO) probe mix (V2.0), incubated at 70°C for 10 minutes, then ramped down to 45°C over 50 minutes (0.5°C/minute). A nuclease digestion followed to remove excess or incorrectly bound DOs at 37°C for 1 hour. The bound DO pairs were then ligated together at 37°C for 1 hour and 15 minutes at 80°C to generate templates for amplification. A 10 µL aliquot of amplification template was transferred to its respective well in the TempO-Seq® PCR Pre-Mix and Primers plate and amplified on the CFX96 thermocycler (Bio-Rad, Mississauga, ON, Canada) with the following program: 37°C for 10 min, 95°C for 1 min; 25 cycles of 95°C for 10 sec, 65°C for 30 sec, 68°C for 30 sec; 68°C for 2 min. For library building and purification, three 96-well plates (288 sample libraries) were pooled together (5 µL per sample) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Cleanup Kit (Clontech Laboratories Inc., Bethlehem, PA, USA) with the adjustments specified by the TempO-Seq® Assay User Guide. The pooled purified TempO-Seq® libraries were then diluted, quantified, and assessed for quality using the Agilent High Sensitivity D1000 TapeStation (Agilent Technologies, Santa Clara, CA, USA) and the qPCR KAPA Library Quantification Kit (Universal qPCR Master Mix) for Illumina NextSeq 500. Samples were sequenced on a total of two NextSeq® 500/550 High Output (75-cycle) flow cells using an Illumina NextSeq® 500 Sequencing Platform (Illumina, San Diego, CA, USA). A separate pool was completed for a fourth plate and an additional 96 sample libraries were added to the sequencing data for subsequent analysis.
The TempO-Seq® Human Surrogate+Tox Panel (S1500+) v2.0 - Index Sets F, G, H were used to index libraries (in two pools)

tag: tissue

value: Spleen

tag: cell line

value: Lymphoblast

tag: chemical long_name

tag: batch

value: Plate 1_IndexF

tag: sequencing pool

value: F

tag: solvent control

tag: well

tag: i7 index_id

value: TAACGCGTC


title: CD3+ T cells, biological rep2

source_name: Human CD3+ T cells

tag: cell type

value: Ctlr


title: GFP-TIS11B_transfection_rep1

tag: genotype


title: CD3+ T cells, NECA-positive, biological rep1

source_name: Human CD3+ T cells activated and cultured with 5'-N-ethylcarboxamidoadenosine (NECA) for three days

value: Positive


title: CD3+ T cells, biological rep3


title: NSACB4_10_+S9_2

tag: chemical

tag: dose

tag: technical control

tag: reference rna

tag: index

value: TGATTAAGC

tag: i5 index_id

value: GCAGATGCA

tag: cas-rn


title: PD_rep2

tag: tissue

value: flesh

tag: age

value: 0 DAP


title: GLKVs01_2_P11

description: SAMPLE 94

data_processing: Fluorescent intensities were loaded and processed for backgroud correction by limma package of R software. Values were log-transformed and normalized by quantile normalization.

source_name: HLA homozygous iPSC

extract_protocol: RNA was extracted by using TRIzol reagent (Thermo Fisher) and purifed by using RNA easy mini kit (QIAGEN).

value: iPSC

tag: gender

tag: source cell

tag: generation method


title: CD3+ T cells, NECA-negative, biological rep3

tag: treatment


title: CD3+ T cells, biological rep1


title: CD3+ T cells, NECA-positive, biological rep2


title: CD3+ T cells, NECA-positive, biological rep3


title: GFP-only transfection_rep3

tag: cell line

value: WT

value: CaPO4 transfection

tag: rip antibody

value: anti-GFP antibody (Abcam ab290)

tag: assay

value: iCLIP-seq


title: CD3+ T cells, NECA-negative, biological rep1

tag: cell type

value: CD3+ T cells

value: Negative


title: R4_RF_rep2

source_name: rind

value: 30 DAP

tag: cultivar


title: GFP-only transfection_rep2

tag: genotype


title: GFP-TIS11B_transfection_rep2

value: CaPO4 transfection with GFP-TIS11B


title: PD_rep1


title: GFP-only transfection_rep1


title: R4_RF_rep1


title: NSACB3_12_+S9_1

value: Spleen

value: Lymphoblast

tag: chemical

tag: chemical long_name

tag: dose

tag: batch

value: Plate 1_IndexF

tag: sequencing pool

tag: technical control

value: F

tag: solvent control

tag: well

tag: i7 index_id

value: AAACACCTT


title: DRXT28s17_3_P13

description: SAMPLE 92

tag: gender

value: Male

tag: source cell

value: PBMC

tag: generation method

value: pCE episomal vector


title: DRXT28s17_2_P13

description: SAMPLE 91

value: iPSC


title: TISgranule_transfected_TIS11B_rep3

data_processing:
Raw reads were trimmed by Trimmomatic (version: 0.39; average quality per base < 15, 4 bp window)
Trimmed reads were mapped to human genome (hg19) using hisat2 (version: 2.1.0)
Reads mapped to each gene were counted by featureCounts (version: 1.6.4)
FPKM value for each gene was calculated by a custom Perl script
Assembly: hg19
Supplementary files format and content: TXT file; Raw read counts for each gene.

extract_protocol:
20 hours after transfection cells were rinsed once with ice cold PBS then scraped in 10 mL ice cold PBS and pelleted at 300g. Pellets from two 10 cm plates were resuspended in 1 mL ice cold hypotonic isolation buffer (225 mM mannitol, 75 mM sucrose, 20 mM Tris-HCl pH 7.4, 0.1 mM EDTA). Cells were lysed with 50 strokes in a 1 mL dounce homogenizer with pestle on ice in order to shear the nuclei from the cytoplasm. Nuclei were pelleted with a two-minute spin at 600g. Subcellular organelles were then pelleted from the supernatant with a 15-minute spin at 7000g and resuspended in ice cold PBS for fluorescence activated particle sorting. Particles were sorted on a BD FACSAria III cell sorter equipped with 70 um nozzle size. mCherry-TIS11B and GFP-SEC61B particles were first detected by fluorescence using the 594 nm and 488 nm excitation lasers respectively, and 405 nm excitation laser for DAPI. A particle gate was drawn to include mCherry-positive or GFP-positive events and DAPI-negative events in order to exclude any remaining nuclei. Particles were then selected for sorting by size and granularity using forward-scattered light (FSC) and side-scattered light (SSC) respectively. The FSC threshold was decreased from 5,000 to 800 in order to visualize subcellular particles. Sorting was performed on purity mode with an average of sorting speed of 150 particles/second. Particles were sorted directly into 1 mL of TRIzol solution in Eppenforf tubes, holding 180,000 particles per tube. RNA-extraction was then performed for each tube separately. Total RNA yield was combined before for library prep. For each replicate about 1.5 million TIS11B granule particles were collected and 2.0 million ER particles. For cytosolic extraction, 20 hours post transfection cells were rinsed once in the dish with ice cold PBS. After aspirating PBS, 400 ul ice cold digitonin solution (40 ug/mL digitonin, 150 mM NaCl, 20 mM HEPES pH 7.4, 0.2 mM EDTA, 2 mM DTT, 2 mM MgCl2) was added and incubated on a shaker at four degrees for ten minutes. After incubation, the digitonin solution now containing the cytosolic extract was pipetted from the plate and spun at 20,000g for one minute to pellet any floating cells. 200 ul of cytosolic extract was added to 1 mL TRIzol solution for RNA extraction.
Library preparation and Illumina sequencing were performed by the MSKCC Integrated Genomics Operations core facility. mRNA libraries were prepared by poly-A selection.The libraries were multiplexed and after paired-end 50 bp sequencing 10-20 million reads per sample were acquired.

treatment_protocol: 24 hours after seeding, cells were transfected by calcium phosphate with either 3ug mCherry-TIS11B or 3 ug GFP-SEC61B per plate

tag: cell line

value: WT

tag: treatment

value: CaPO4 transfection with mCherry-TIS11B

tag: cell compartment

value: TISgranule


title: NSACB2_28_+S9_2

tag: tissue

tag: cell type

tag: reference rna

tag: index

value: TGATTAAGC

tag: i5 index_id

value: ACAACCATC

tag: cas-rn


title: R2_RF_rep2

value: flesh

tag: age

tag: cultivar


title: R2_RF_rep1

value: 30 DAP


title: NSACB4_10_+S9_1

tag: chemical

tag: chemical long_name

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

tag: solvent control

value: AGCAAGGTC


title: NSACB2_28_+S9_1

value: Spleen

tag: cell line

tag: treatment

tag: well

tag: i7 index_id

value: GTGCATTAG


title: TISgranule_transfected_TIS11B_rep2

tag: genotype

tag: cell compartment


title: NSACB3_12_+S9_2

tag: tissue

tag: cell type

value: Lymphoblast

value: Plate 1_IndexF

tag: reference rna

tag: index

tag: i5 index_id

value: TTCCGAATT


title: NSACB5_1250_+S9_2

tag: chemical

tag: chemical long_name

value: F

value: TCAGCTAAT

value: AAGTAGGCT

tag: cas-rn


title: NSACB4_14_+S9_2

tag: dose

tag: batch

tag: sequencing pool

value: GCAGATGCA


title: R4_CT_rep1

tag: age

value: 20 DAP

tag: cultivar


title: W_RF_rep1

value: Citrullus lanatus germplasm PI296341FR


title: NSACB5_1250_+S9_1

tag: cell line

tag: treatment

tag: technical control

tag: solvent control

tag: well

value: TAACGCGTC


title: ER_transfected_SEC61B_rep2

tag: genotype

value: WT

value: CaPO4 transfection with GFP-SEC61B

tag: cell compartment

value: ER


title: Cytosol_untransfected_rep2

value: cytosol


title: DRXT28s10_3_P13

description: SAMPLE 86

tag: cell type

value: iPSC

tag: gender

value: Male

tag: source cell

value: PBMC

tag: generation method

value: pCE episomal vector


title: DRXT28s15_1_P13

description: SAMPLE 87


title: DRXT28s17_1_P13

description: SAMPLE 90


title: DRXT28s15_2_P13

description: SAMPLE 88


title: DRXT28s15_3_P13

description: SAMPLE 89


title: ER_transfected_SEC61B_rep1


title: NSACB4_14_+S9_1

tag: tissue

value: Spleen

value: Lymphoblast

tag: chemical

tag: chemical long_name

value: Plate 1_IndexF

tag: reference rna

tag: i7 index_id

tag: index

tag: i5 index_id

value: AGCAAGGTC

tag: cas-rn


title: W_BW_rep1

value: flesh

tag: age

value: 10 DAP


title: Cytosol_untransfected_rep1

tag: cell line

tag: treatment


title: DRXT28s10_2_P13

description: SAMPLE 85


title: C_RF_rep1

value: 30 DAP

tag: genotype


title: NSACB3_16_+S9_2

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

value: F

tag: solvent control

tag: well

value: TCAGCTAAT

value: TTCCGAATT


title: DRXT28s10_1_P13

description: SAMPLE 84

tag: cell type

tag: gender

tag: source cell

tag: generation method


title: TISgranule_transfected_TIS11B_rep1

value: WT

value: CaPO4 transfection with mCherry-TIS11B

tag: cell compartment

value: TISgranule


title: R4_CT_rep2

tag: tissue

value: 20 DAP

tag: cultivar


title: WCL_utransfected

value: whole cell


title: DRXT28s05_3_P13

description: SAMPLE 83

value: iPSC

value: Male

value: PBMC


title: NSACB3_16_+S9_1

value: Spleen

value: Lymphoblast

tag: chemical

tag: chemical long_name

tag: reference rna

tag: i7 index_id

tag: index

tag: i5 index_id

value: AAACACCTT

tag: cas-rn


title: 5_Aza_rep3

value: flesh

tag: age

tag: genotype

value: 5-zazcytidine treatment


title: MV4;11 BFA-4

first: Hsin-Che

last: Huang

address: 417 E 68th St

department: Chemical Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Differential expression analysis was performed using DESeq2. The Wald test was used to generate p-values and log2 fold changes.
Assembly: GRCh38
Supplementary files format and content: raw_counts.csv: Matrix table with raw gene counts for every gene and every sample.

growth_protocol: MV4;11 CASP1 KO cells were grown and maintained in RPMI 1640 medium with 2 mM L-glutamine and 10% fetal bovine serum (FBS). Cell line was regularly tested for mycoplasma.

extract_protocol:
Cellular RNA was extracted using the RNeasy Mini Kit (Qiagen) and residual genomic DNA was removed by on-membrane DNase digestion (Qiagen) per the manufacturer's protocol.
RNA libraries with polyA selection were prepared for sequencing using Illumina standard protocol.

treatment_protocol: MV4;11 CASP1 KO cells were treated with DMSO, methyl bestatin, or brefeldin A for 6 hours, each in quadruplicates.

tag: cell line

value: macrophage

value: CASP1 knockout

tag: treatment

value: brefeldin A


title: DRXT28s05_2_P13

description: SAMPLE 82

tag: cell type

tag: gender

value: pCE episomal vector


title: NSACB2_39_+S9_2

tag: dose

tag: batch

value: Plate 1_IndexF

tag: sequencing pool

tag: technical control

value: F

tag: solvent control

tag: well

value: TCAGCTAAT

value: ACAACCATC


title: DRXT28s05_1_P13

description: SAMPLE 81

tag: source cell

tag: generation method


title: MV4;11 BFA-3


title: 5_Aza_rep2

tag: tissue

value: 20 DAP


title: MV4;11 BFA-2


title: NSACB2_39_+S9_1

tag: chemical

tag: chemical long_name

tag: reference rna

tag: i7 index_id

tag: index

tag: i5 index_id

value: GTGCATTAG


title: DRXT28s04_2_P13

description: SAMPLE 79

tag: cell type

value: iPSC

value: Male


title: DRXT28s04_3_P13

description: SAMPLE 80

tag: gender

value: PBMC


title: MV4;11 BFA-1

tag: cell line

tag: genotype

tag: treatment


title: DRXT28s04_1_P13

description: SAMPLE 78


title: Mock_rep3

tag: age

value: Wild-type


title: NSACB5_1768_+S9_1

value: Spleen

value: Lymphoblast

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

tag: solvent control

value: TGCTTATTC

value: TAACGCGTC

tag: cas-rn


title: 5_Aza_rep1

tag: tissue

value: flesh

value: 5-zazcytidine treatment


title: MV4;11 MeBs-3

value: macrophage

value: CASP1 knockout

value: methyl bestatin


title: NSACB4_20_+S9_2

tag: chemical

tag: chemical long_name

value: Plate 1_IndexF

value: F

tag: reference rna

tag: well

value: GCAGATGCA


title: Mock_rep2

value: 20 DAP


title: MV4;11 MeBs-4

tag: cell type


title: NSACB4_20_+S9_1

tag: i7 index_id

tag: index

tag: i5 index_id

value: AGCAAGGTC


title: DRXT18s11_3_P13

description: SAMPLE 77

value: iPSC

tag: gender

value: Male

tag: source cell

tag: generation method

value: pCE episomal vector


title: MV4;11 MeBs-2

tag: cell line

tag: genotype

tag: treatment


title: DRXT18s11_2_P13

description: SAMPLE 76

value: PBMC


title: RF_rep3

tag: age

value: 30 DAP


title: NSACB3_23_+S9_2

value: Spleen

value: Lymphoblast

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

tag: solvent control

value: TGCTTATTC

value: TTCCGAATT

tag: cas-rn


title: C_BW_rep1

tag: tissue

value: flesh

value: 10 DAP


title: MV4;11 MeBs-1

tag: cell type

value: macrophage

value: CASP1 knockout

value: methyl bestatin


title: DRXT18s11_1_P13

description: SAMPLE 75


title: RF_rep2


title: NSACB3_23_+S9_1

tag: chemical

tag: chemical long_name

value: Plate 1_IndexF

value: F

tag: reference rna

tag: well

tag: i7 index_id

tag: index

value: AAACACCTT


title: MV4;11 DMSO-4

tag: cell line

tag: genotype

value: DMSO


title: NSACB5_1768_+S9_2

tag: treatment

tag: i5 index_id

value: AAGTAGGCT


title: DRXT18s08_3_P13

description: SAMPLE 74

value: iPSC

tag: gender

value: Male

tag: source cell

tag: generation method

value: pCE episomal vector


title: Mock_rep1

tag: age

value: 20 DAP

value: Wild-type


title: GLKVs01_1_P11

description: SAMPLE 93

value: Cord blood


title: MV4;11 DMSO-3


title: MV4;11 DMSO-2


title: DRXT18s08_1_P13

description: SAMPLE 72

value: PBMC


title: NSACB2_55_+S9_2

value: Spleen

value: Lymphoblast

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

tag: solvent control

value: TGCTTATTC

value: ACAACCATC

tag: cas-rn


title: NSACB2_55_+S9_1

tag: tissue

tag: cell type

tag: chemical

tag: chemical long_name

tag: reference rna

tag: well

value: GTGCATTAG


title: CT_rep2

value: flesh

tag: genotype


title: CT_rep3


title: MV4;11 DMSO-1

tag: cell line

value: macrophage

value: CASP1 knockout

tag: treatment


title: DRXT18s08_2_P13

description: SAMPLE 73

tag: gender

tag: source cell

tag: generation method


title: DRXT18s06_3_P13

description: SAMPLE 71


title: normal cells in normoxia, cultured in low serum conditions (hashtag oligo)

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

library_source: other

data_processing:
Reads were aligned to GRCh38 and count matrix for features were calculated using cellranger 3.1.0
Seurat 4.0.1 was used for downstream analysis, including removing doublets and negatives, other cell filtering, PCA, tSNE and Umap and clustering
Assembly: GRCh38
Supplementary files format and content: Seurat R object

molecule: other

source_name: primary patient-derived cell cultures (tumour-adjacent normal kidney)

growth_protocol: Primary renal cell cultures were generated from freshly excised ccRCC tissue and tumor-adjacent normal kidney. All samples were from the same patient, and the tumour samples were taken from different regions of the same tumour. Briefly, tissue blocks were minced, incubated with 193U/ml Collagenase II and 3.33ug/ml DNase I for one hour at 37 °C with agitation every 5 minutes, and sequentially passed through 100um, 70um and 40um filters. Cell pellets were resuspended in growth medium (DMEM/F12 1:1, supplemented with L-glutamax, penicillin-streptomycin, insulin-transferrin-sodium selenite, 4 ng/ml triiodo-L-thyronine, 100 ng/ml epidermal growth factor, 36 ng/ml hydrocortisone and 10% fetal bovine serum*) and plated on gelatinized dishes. Experiments were performed after the 2nd or 3rd passage. *Except the low serum conditions sample, which was cultured in the same medium but with 0.5% fetal bovine serum.

extract_protocol:
Primary cell cultures were detached and made into single cell suspensions using TrypLE Express (Thermo Scientific) with pipetting. Single cell suspensions were incubated with TotalSeq-A ‘hashtag’ antibodies (1ug antibody with approximately 5x10E5 cells) to enable multiplexing. The hashtag antibodies and the barcode sequences were anti-human 1 (GTCAACTCTTTAGCG), anti-human 2 (TGATGGCCTATTGGG), anti-human 3 (TTCCGCCTCTCTTTG), anti-human 4 (AGTAAGTTCAGCGTA) and anti-human 5 (AAGTATCGTTTCGCA). Cell viability and concentration were assessed using Trypan Blue and a TC10 automated cell counter (Bio-Rad). 2500 cells from each sample were pooled, loaded onto a single channel of a 10x genomics 3' GEX chip for GEM generation as per the 10x genomics 3' GEX protocol (GEX-v3.1 chemistry).
Single cell 3’ GEX RNA libraries were prepared according to manufacturer’s instructions (10x genomics, GEX-v3.1 chemistry, single index).

treatment_protocol: Hypoxia incubations were performed at 0.5% O2 for 16 hours in a hypoxia chamber (In Vivo2 400 Hypoxia Work Station, Ruskinn Technology).

value: n/a hashtag oligo

tag: ambient o2 concentration

tag: sequenced molecule

value: Hashtag Oligo

tag: hashtag number

value: Hashtag 5


title: NSACB5_2500_+S9_2

first: Matthew

address: 251 Sir Frederick Banting Driveway

institute: Government of Canada

tag: dose

tag: batch

value: Plate 1_IndexF

tag: sequencing pool

tag: technical control

value: F

tag: solvent control

tag: i7 index_id

tag: index

value: ATTCGAATC

tag: i5 index_id

value: AAGTAGGCT


title: NSACB5_2500_+S9_1

tag: tissue

tag: cell type

tag: chemical

tag: chemical long_name

tag: reference rna

tag: well

value: TAACGCGTC

tag: cas-rn


title: NSACB4_28_+S9_2

tag: cell line

tag: treatment

value: GCAGATGCA


title: tumour cells from tumour region 2 (hashtag oligo)

source_name: primary patient-derived cell cultures (ccRCC tumour)

tag: ambient o2 concentration

tag: sequenced molecule

tag: hashtag number

value: Hashtag 4


title: DRXT18s06_1_P13

description: SAMPLE 69

value: iPSC

tag: gender

value: Male

tag: source cell

value: PBMC

tag: generation method

value: pCE episomal vector


title: DRXT18s06_2_P13

description: SAMPLE 70


title: NSACB4_28_+S9_1

value: Spleen

value: Lymphoblast

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

tag: solvent control

tag: i7 index_id

tag: index

value: AGCAAGGTC


title: tumour cells from tumour region 1 (hashtag oligo)

tag: cell type

value: n/a hashtag oligo

value: Hashtag 3


title: RF_rep1

tag: tissue

value: flesh

tag: age

value: 30 DAP

tag: genotype


title: NSACB3_33_+S9_2

tag: cell line

tag: chemical

tag: chemical long_name

tag: treatment

value: Plate 1_IndexF

value: F

tag: reference rna

tag: well

tag: i5 index_id

value: TTCCGAATT

tag: cas-rn


title: normal cells in hypoxia (hashtag oligo)

tag: ambient o2 concentration

tag: sequenced molecule

value: Hashtag Oligo

tag: hashtag number

value: Hashtag 2


title: DRXT18s05_3_P13

description: SAMPLE 68

tag: gender

tag: source cell

tag: generation method


title: skin and hair follicle, Sphere keratin 1

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

description: Gene expression data after 20 days topical application

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse. GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) for the top DEGs.
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CEL files ).
RMA signal

organism: Mus

source_name: skin treated with microshpere keratin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: C57BL6 mice (seven-weeks-old) was used in this experiment.

extract_protocol: The treated skin from all groups were collected cut into pieces and RNA was extracted using ISOGEN solution (Nippon Gene Co. Ltd., Toyama, Japan).

treatment_protocol: Six-weeks-old male C57BL/6 mice. An acclimatization period of seven days was granted to the mice, and four groups (n = 5) were randomly formed before proceeding with the hair growth experiment. We distinguish, untreatedgroup (MilliQ water), 1% minoxidil (minox, positive control), 1% keratin, and 1% microsphere (sphere keratin). The hair was trimmed and depleted and the treatments were applied topically for 20 day before sacrifice by cervical spine dislocation. We collected then the treated skin for further molecular analysis

tag: strain

tag: tissue

value: skin and hair follicle

value: microsphere keratin

tag: time

value: after 20 days topical application


title: DRXT18s05_2_P13

first: Masayoshi

address: Shogoin kawahara-cho, sakyo-ku,

institute: CiRA foundation

description: SAMPLE 67

tag: cell type

value: iPSC

value: Male

value: PBMC


title: skin and hair follicle, Keratin 2

source_name: skin treated with keratin

value: keratin


title: NSACB3_33_+S9_1

last: Meier

value: Spleen

tag: cell line

value: Lymphoblast

tag: chemical

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

tag: solvent control

tag: i7 index_id

tag: index

value: ATTCGAATC

value: AAACACCTT


title: DRXT18s03_3_P13

description: SAMPLE 65

value: pCE episomal vector


title: DRXT18s03_2_P13

description: SAMPLE 64


title: DRXT18s05_1_P13

description: SAMPLE 66


title: NSACB2_78_+S9_1

tag: chemical long_name

tag: treatment

value: Plate 1_IndexF

tag: reference rna

tag: well

tag: i5 index_id

value: GTGCATTAG

tag: cas-rn


title: skin and hair follicle, Keratin 1

tag: strain

tag: tissue

tag: time


title: DRXT18s03_1_P13

description: SAMPLE 63

tag: cell type

tag: gender

tag: source cell

tag: generation method


title: NSACB5_3536_+S9_2

tag: cell line

tag: chemical

tag: dose

tag: batch

tag: sequencing pool

tag: technical control

value: F

value: ATCGCGACT

value: AAGTAGGCT


title: skin and hair follicle, minox 2

source_name: skin treated with minoxidil

value: skin and hair follicle

tag: treatment

value: minoxidil


title: DRXT18s02_3_P13

description: SAMPLE 62


title: NSACB4_39_+S9_2

tag: chemical long_name

tag: reference rna

tag: solvent control

tag: well

tag: i7 index_id

tag: index

value: GCAGATGCA


title: skin and hair follicle, Sphere keratin 2

tag: strain

tag: tissue

value: microsphere keratin

tag: time

value: after 20 days topical application


title: normal cells in normoxia (hashtag oligo)

tag: cell type

value: n/a hashtag oligo

tag: ambient o2 concentration

tag: sequenced molecule

value: Hashtag Oligo

tag: hashtag number

value: Hashtag 1