title: RNA-seq, leaf, J2_216, chemical fertilizer, Year 2023

description:
Library name: Ogawa_270
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_216


title: RNA-seq, leaf, J2_293, chemical fertilizer, Year 2023

status: Public on Jan 16 2026

type: SRA

city: Tsukuba

first: Hirofunmi

last: Fukuda

state: Ibaraki

address: 1-31-1 Kannondai

country: Japan

institute: National Agriculture and Food Research Organization (NARO)

description:
Library name: Ogawa_273
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_293

library_source: transcriptomic

data_processing:
The libraries were sequenced using the Illumina NovaSeq X Plus. Sequencing was performed on the 25B flow cell with paired-end 150-bp and unique dual-index reads. The reads were preprocessed by CLC Genomics Workbench version 25.0 (Qiagen). Reads were first trimmed using the following parameters: quality limit of 0.05, maximum number of ambiguities 2. Next, raw reads were mapped to the genome assembly and gene sets of “Os-Nipponbare-Reference-IRGSP-1.0" with the following parameters: mismatch cost of 2, insertion–deletion cost of 3, length fraction of 0.8, similarity fraction of 0.8, and maximum number of hits of a read of 10. Then, uniquely mapped read counts were quantified. Genes with at least one raw read count in all of the library samples for each comparison were analyzed.
Assembly: Os-Nipponbare-IRGSP-1.0
Supplementary files format and content: csv file includes RNA-seq raw count on whole transcripts for each sample.

molecule: polyA RNA

organism: Oryza sativa

source_name: leaf

growth_protocol: A hundred of  JAM2 lines (F5 and F6) in 2022 and 2023 were used in this study. Seeds soaked in water at 30°C for 2 days were sown in trays filled with soils and incubated at 30°C in the dark for 2 days. Seedlings were grown in a paddy field in Kannondai, Tsukuba, for a month, and then 33 seedlings per line were transplanted (11 plants 18 cm apart × 3 rows 30 cm apart, no replicates) into a nearby paddy field and cultivated for 5 months The dates of sowing was April 18 in 2022 and April 17 in 2023.

extract_protocol:
The most expanded leaf was collected from 9:00 to 11:00 am as one biological replicate, immediately frozen in liquid N, and stored at -80 °C until sample crushing. Frozen samples were crushed by multi-specimen cell disruption device (BMS-A20TP, BMS) just before RNA extraction. Total RNAs from each sample were extracted using RNeasy Plant Mini Kit (QIAGEN), referring to the manufacture’s protocol. One biological replicate was obtained for each JAM2 line at 6 weeks after transplanting:  July 1, 2022 and June 29, 2023.
RNA-sequencing (RNA-seq) libraries were prepared using the NEBNext Ultra II Directional mRNA-seq kit for Illumina (New England Biolabs), following the manufacturer’s protocols.

treatment_protocol: Chemical fertilizer was applied as a basal dressing at 56:176:56:90:120 kg/ha (N:PO4:K:Mg:SiO2).

tag: tissue

value: leaf

tag: genotype

value: Akidawara x Iwaidawara x Tachiharuka x Toyomeki

tag: treatment

value: control


title: UVA119  Coronary artery bulk ATAC

city: Charlottesville

first: Clint

middle: L

last: Miller

state: VA

department: Center for Public Health Genomics

country: USA

institute: University of Virginia

description: UVA119 _ATAC

library_source: genomic

data_processing:
Bulk ATAC-seq sample processing was all conducted using the PEPATAC pipeline (version 0.8.6). This includes alignment, duplicate removal, mitochondrial read removal, and peak-calling.
Assembly: hg38
Supplementary files format and content: Supplementary_files_format_and_content: narrowPeak (peaks from each individual sample)

molecule: genomic DNA

organism: Homo sapiens

source_name: human coronary artery

extract_protocol:
Frozen coronary artery segments were broken down into small pieces using mortar and pestle under dry ice and liquid nitrogen. Nuclei were isolated using iodixanol/sucrose gradients following the Omni-ATAC protocol (Corces et al. Nature Methods 2017). 50,000 nuclei were washed in cold ATAC Resuspension Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) + 0.1% Tween-20 and centrifuged for 10 minutes at 500 g at 4°C. 50,000 nuclei were then resuspended in 50 µl of transposition mix (25 µl 2X TD buffer, 2.5 µl of Tn5 transposase (Illumina), 16.5 µl PBS, 0.01% digitonon, 0.1% Tween-20). Samples were subsequently transposed for 30 minutes at 37°C with shaking (1000 rpm).
50,000 nuclei per sample were used for Tn5 transposition reactions, incubated for 30 minutes at 37C. Transposed DNA was purified using the Zymo DNA Clean and Concentrator-5 Kit and bulk ATAC-seq libraries were generated by PCR amplification and uniquely indexed barcodes. Bulk ATAC-seq libraries were sequenced on an Illumina NovaSeq 6000.
Transposed DNA was first purified using the Zymo DNA Clean and Concentrator-5 Kit. Libraries were subsequently constructed and amplified according to Supplementary Protocol 1 in the Omni-ATAC protocol (Corces et al. Nature Methods 2017). Each library underwent 5 cycles of pre-amplification and then additional amplification cycles (determined by qPCR of pre-amplified mixtures)

treatment_protocol: Human hearts were obtained from heart transplant recipients or rejected donor hearts. Hearts were all placed in cardioplegic solution prior to dissection of the left anterior descending (LAD), left circumflex (LCX), and right coronary arteries (RCA). All coronary artery samples were flash frozen in liquid nitrogen in the same manner

value: human coronary artery

value: ATAC-Seq


title: RNA-seq, leaf, J2_312, chemical fertilizer, Year 2023

description:
Library name: Ogawa_271
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_312


title: RNA-seq, leaf, J2_316, chemical fertilizer, Year 2023

description:
Library name: Ogawa_274
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_316


title: RNA-seq, leaf, J2_307, chemical fertilizer, Year 2023

description:
Library name: Ogawa_269
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_307


title: RNA-seq, leaf, J2_368, chemical fertilizer, Year 2023

description:
Library name: Ogawa_267
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_368


title: RNA-seq, leaf, J2_203, chemical fertilizer, Year 2023

description:
Library name: Ogawa_266
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_203


title: RNA-seq, leaf, J2_335, chemical fertilizer, Year 2023

description:
Library name: Ogawa_268
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_335


title: RNA-seq, leaf, J2_322, chemical fertilizer, Year 2023

description:
Library name: Ogawa_265
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_322


title: UVA113  Coronary artery bulk ATAC

description: UVA113 _ATAC


title: kidney biopsy_NH292

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

molecule: total RNA

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array (Affymetrix, Santa Clara, CA).

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: mmdx (abmr/mixed, no abmr/mixed)

value: ABMR/Mixed

value: kidney biopsy


title: UVA115  Coronary artery bulk ATAC

description: UVA115 _ATAC


title: UVA116  Coronary artery bulk ATAC

description: UVA116 _ATAC


title: UVA112  Coronary artery bulk ATAC

description: UVA112 _ATAC


title: kidney biopsy_NH287

value: No ABMR/Mixed


title: kidney biopsy_NH284


title: kidney biopsy_NH285


title: kidney biopsy_NH290


title: kidney biopsy_NH283


title: kidney biopsy_NH288


title: RNA-seq, leaf, J2_248, chemical fertilizer, Year 2023

description:
Library name: Ogawa_263
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_248


title: RNA-seq, leaf, J2_256, chemical fertilizer, Year 2023

description:
Library name: Ogawa_264
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_256


title: RNA-seq, leaf, J2_251, chemical fertilizer, Year 2023

description:
Library name: Ogawa_262
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_251


title: RNA-seq, leaf, J2_372, chemical fertilizer, Year 2023

description:
Library name: Ogawa_259
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_372


title: RNA-seq, leaf, J2_231, chemical fertilizer, Year 2023

description:
Library name: Ogawa_256
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_231


title: UVA111  Coronary artery bulk ATAC

description: UVA111 _ATAC


title: RNA-seq, leaf, J2_280, chemical fertilizer, Year 2023

description:
Library name: Ogawa_257
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_280


title: kidney biopsy_NH281


title: RNA-seq, leaf, J2_294, chemical fertilizer, Year 2023

description:
Library name: Ogawa_255
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_294


title: RNA-seq, leaf, J2_326, chemical fertilizer, Year 2023

description:
Library name: Ogawa_260
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_326


title: RNA-seq, leaf, J2_204, chemical fertilizer, Year 2023

description:
Library name: Ogawa_261
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_204


title: UVA108  Coronary artery bulk ATAC

description: UVA108 _ATAC


title: kidney biopsy_NH302


title: UVA107  Coronary artery bulk ATAC

description: UVA107 _ATAC


title: kidney biopsy_NH278


title: kidney biopsy_NH277


title: UVA104  Coronary artery bulk ATAC

description: UVA104 _ATAC


title: kidney biopsy_NH282


title: kidney biopsy_NH280


title: RNA-seq, leaf, J2_212, chemical fertilizer, Year 2023

description:
Library name: Ogawa_254
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_212


title: RNA-seq, leaf, J2_352, chemical fertilizer, Year 2023

description:
Library name: Ogawa_250
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_352


title: UVA103  Coronary artery bulk ATAC

description: UVA103 _ATAC


title: UVA106  Coronary artery bulk ATAC

description: UVA106 _ATAC


title: RNA-seq, leaf, J2_282, chemical fertilizer, Year 2023

description:
Library name: Ogawa_252
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_282


title: RNA-seq, leaf, J2_288, chemical fertilizer, Year 2023

description:
Library name: Ogawa_251
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_288


title: kidney biopsy_NH276


title: RNA-seq, leaf, J2_319, chemical fertilizer, Year 2023

description:
Library name: Ogawa_253
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_319


title: RNA-seq, leaf, J2_236, chemical fertilizer, Year 2023

description:
Library name: Ogawa_249
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_236


title: UVA102  Coronary artery bulk ATAC

description: UVA102 _ATAC


title: RNA-seq, leaf, J2_213, chemical fertilizer, Year 2023

description:
Library name: Ogawa_245
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_213


title: RNA-seq, leaf, J2_250, chemical fertilizer, Year 2023

description:
Library name: Ogawa_248
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_250


title: RNA-seq, leaf, J2_345, chemical fertilizer, Year 2023

description:
Library name: Ogawa_247
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_345


title: kidney biopsy_NH275


title: UVA101  Coronary artery bulk ATAC

description: UVA101 _ATAC


title: kidney biopsy_NH274


title: RNA-seq, leaf, J2_364, chemical fertilizer, Year 2023

description:
Library name: Ogawa_246
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_364


title: UVA100  Coronary artery bulk ATAC

description: UVA100 _ATAC


title: kidney biopsy_NH273


title: RNA-seq, leaf, J2_210, chemical fertilizer, Year 2023

description:
Library name: Ogawa_244
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_210


title: UVA099  Coronary artery bulk ATAC

description: UVA099 _ATAC


title: UVA098  Coronary artery bulk ATAC

description: UVA098 _ATAC


title: RNA-seq, leaf, J2_285, chemical fertilizer, Year 2023

description:
Library name: Ogawa_242
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_285


title: kidney biopsy_NH272


title: RNA-seq, leaf, J2_270, chemical fertilizer, Year 2023

description:
Library name: Ogawa_241
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_270


title: RNA-seq, leaf, J2_226, chemical fertilizer, Year 2023

description:
Library name: Ogawa_240
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_226


title: RNA-seq, leaf, J2_245, chemical fertilizer, Year 2023

description:
Library name: Ogawa_239
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_245


title: RNA-seq, leaf, J2_310, chemical fertilizer, Year 2023

description:
Library name: Ogawa_243
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_310


title: UVA096  Coronary artery bulk ATAC

description: UVA096 _ATAC


title: RNA-seq, leaf, J2_287, chemical fertilizer, Year 2023

description:
Library name: Ogawa_238
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_287


title: UVA094  Coronary artery bulk ATAC

description: UVA094 _ATAC


title: kidney biopsy_NH270


title: RNA-seq, leaf, J2_277, chemical fertilizer, Year 2023

description:
Library name: Ogawa_237
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_277


title: kidney biopsy_NH289


title: RNA-seq, leaf, J2_202, chemical fertilizer, Year 2023

description:
Library name: Ogawa_234
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_202


title: RNA-seq, leaf, J2_246, chemical fertilizer, Year 2023

description:
Library name: Ogawa_233
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_246


title: UVA091  Coronary artery bulk ATAC

description: UVA091 _ATAC


title: kidney biopsy_NH279


title: UVA088  Coronary artery bulk ATAC

description: UVA088 _ATAC


title: kidney biopsy_NH268


title: kidney biopsy_NH307


title: kidney biopsy_NH267


title: RNA-seq, leaf, J2_233, chemical fertilizer, Year 2023

description:
Library name: Ogawa_230
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_233


title: UVA087  Coronary artery bulk ATAC

description: UVA087 _ATAC


title: UVA086  Coronary artery bulk ATAC

description: UVA086 _ATAC


title: RNA-seq, leaf, J2_260, chemical fertilizer, Year 2023

description:
Library name: Ogawa_229
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_260


title: RNA-seq, leaf, J2_206, chemical fertilizer, Year 2023

description:
Library name: Ogawa_228
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_206


title: kidney biopsy_NH296


title: kidney biopsy_NH286


title: RNA-seq, leaf, J2_252, chemical fertilizer, Year 2023

description:
Library name: Ogawa_232
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_252


title: RNA-seq, leaf, J2_275, chemical fertilizer, Year 2023

description:
Library name: Ogawa_227
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_275


title: RNA-seq, leaf, J2_235, chemical fertilizer, Year 2023

description:
Library name: Ogawa_231
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_235


title: kidney biopsy_NH264


title: RNA-seq, leaf, J2_262, chemical fertilizer, Year 2023

description:
Library name: Ogawa_236
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_262


title: RNA-seq, leaf, J2_221, chemical fertilizer, Year 2023

description:
Library name: Ogawa_223
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_221


title: RNA-seq, leaf, J2_218, chemical fertilizer, Year 2023

description:
Library name: Ogawa_222
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_218


title: kidney biopsy_NH308


title: kidney biopsy_NH269


title: kidney biopsy_NH266


title: UVA082  Coronary artery bulk ATAC

description: UVA082 _ATAC


title: kidney biopsy_NH315


title: kidney biopsy_NH271


title: kidney biopsy_NH262


title: kidney biopsy_NH265


title: RNA-seq, leaf, J2_273, chemical fertilizer, Year 2023

description:
Library name: Ogawa_217
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_273


title: UVA085  Coronary artery bulk ATAC

description: UVA085 _ATAC


title: RNA-seq, leaf, J2_227, chemical fertilizer, Year 2023

description:
Library name: Ogawa_218
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_227


title: RNA-seq, leaf, J2_229, chemical fertilizer, Year 2023

description:
Library name: Ogawa_235
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_229


title: kidney biopsy_NH261


title: kidney biopsy_NH263


title: RNA-seq, leaf, J2_209, chemical fertilizer, Year 2023

description:
Library name: Ogawa_226
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_209


title: RNA-seq, leaf, J2_264, chemical fertilizer, Year 2023

description:
Library name: Ogawa_221
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_264


title: RNA-seq, leaf, J2_274, chemical fertilizer, Year 2023

description:
Library name: Ogawa_225
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_274


title: UVA079  Coronary artery bulk ATAC

description: UVA079 _ATAC


title: UVA084  Coronary artery bulk ATAC

description: UVA084 _ATAC


title: UVA078  Coronary artery bulk ATAC

description: UVA078 _ATAC


title: UVA080  Coronary artery bulk ATAC

description: UVA080 _ATAC


title: UVA074  Coronary artery bulk ATAC

description: UVA074 _ATAC


title: RNA-seq, leaf, J2_225, chemical fertilizer, Year 2023

description:
Library name: Ogawa_219
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_225


title: UVA081  Coronary artery bulk ATAC

description: UVA081 _ATAC


title: RNA-seq, leaf, J2_226, chemical fertilizer, Year 2022

description:
Library name: J2_226
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_226


title: RNA-seq, leaf, J2_245, chemical fertilizer, Year 2022

description:
Library name: J2_245
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_245


title: RNA-seq, leaf, J2_255, chemical fertilizer, Year 2023

description:
Library name: Ogawa_220
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_255


title: RNA-seq, leaf, J2_211, chemical fertilizer, Year 2022

description:
Library name: J2_211
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_211


title: RNA-seq, leaf, J2_203, chemical fertilizer, Year 2022

description:
Library name: J2_203
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_203


title: kidney biopsy_NH257


title: RNA-seq, leaf, J2_337, chemical fertilizer, Year 2022

description:
Library name: J2_337
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_337


title: kidney biopsy_NH260


title: RNA-seq, leaf, J2_231, chemical fertilizer, Year 2022

description:
Library name: J2_231
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_231


title: RNA-seq, leaf, J2_415, chemical fertilizer, Year 2022

description:
Library name: J2_415
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_415


title: RNA-seq, leaf, J2_256, chemical fertilizer, Year 2022

description:
Library name: J2_256
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_256


title: kidney biopsy_NH259


title: RNA-seq, leaf, J2_326, chemical fertilizer, Year 2022

description:
Library name: J2_326
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_326


title: kidney biopsy_NH258


title: UVA072  Coronary artery bulk ATAC

description: UVA072 _ATAC


title: RNA-seq, leaf, J2_365, chemical fertilizer, Year 2022

description:
Library name: J2_365
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_365


title: kidney biopsy_NH256


title: RNA-seq, leaf, J2_251, chemical fertilizer, Year 2022

description:
Library name: J2_251
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_251


title: RNA-seq, leaf, J2_370, chemical fertilizer, Year 2022

description:
Library name: J2_370
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_370


title: UVA071  Coronary artery bulk ATAC

description: UVA071 _ATAC


title: kidney biopsy_NH253


title: kidney biopsy_NH254


title: kidney biopsy_NH255


title: UVA069  Coronary artery bulk ATAC

description: UVA069 _ATAC


title: UVA070  Coronary artery bulk ATAC

description: UVA070 _ATAC


title: RNA-seq, leaf, J2_345, chemical fertilizer, Year 2022

description:
Library name: J2_345
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_345


title: RNA-seq, leaf, J2_374, chemical fertilizer, Year 2022

description:
Library name: J2_374
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_374


title: UVA073  Coronary artery bulk ATAC

description: UVA073 _ATAC


title: RNA-seq, leaf, J2_364, chemical fertilizer, Year 2022

description:
Library name: J2_364
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_364


title: kidney biopsy_NH252


title: RNA-seq, leaf, J2_368, chemical fertilizer, Year 2022

description:
Library name: J2_368
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_368


title: UVA068  Coronary artery bulk ATAC

description: UVA068 _ATAC


title: RNA-seq, leaf, J2_414, chemical fertilizer, Year 2022

description:
Library name: J2_414
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_414


title: RNA-seq, leaf, J2_400, chemical fertilizer, Year 2022

description:
Library name: J2_400
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_400


title: kidney biopsy_NH250


title: UVA066  Coronary artery bulk ATAC

description: UVA066 _ATAC


title: RNA-seq, leaf, J2_306, chemical fertilizer, Year 2022

description:
Library name: J2_306
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_306


title: UVA067  Coronary artery bulk ATAC

description: UVA067 _ATAC


title: kidney biopsy_NH251


title: RNA-seq, leaf, J2_359, chemical fertilizer, Year 2022

description:
Library name: J2_359
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_359


title: RNA-seq, leaf, J2_315, chemical fertilizer, Year 2022

description:
Library name: J2_315
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_315


title: RNA-seq, leaf, J2_382, chemical fertilizer, Year 2022

description:
Library name: J2_382
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_382


title: RNA-seq, leaf, J2_298, chemical fertilizer, Year 2022

description:
Library name: J2_298
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_298


title: RNA-seq, leaf, J2_316, chemical fertilizer, Year 2022

description:
Library name: J2_316
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_316


title: kidney biopsy_NH248


title: kidney biopsy_NH249


title: UVA065  Coronary artery bulk ATAC

description: UVA065 _ATAC


title: UVA064  Coronary artery bulk ATAC

description: UVA064 _ATAC


title: RNA-seq, leaf, J2_319, chemical fertilizer, Year 2022

description:
Library name: J2_319
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_319


title: UVA062  Coronary artery bulk ATAC

description: UVA062 _ATAC


title: RNA-seq, leaf, J2_387, chemical fertilizer, Year 2022

description:
Library name: J2_387
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_387


title: RNA-seq, leaf, J2_411, chemical fertilizer, Year 2022

description:
Library name: J2_411
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_411


title: RNA-seq, leaf, J2_287, chemical fertilizer, Year 2022

description:
Library name: J2_287
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_287


title: UVA063  Coronary artery bulk ATAC

description: UVA063 _ATAC


title: RNA-seq, leaf, J2_349, chemical fertilizer, Year 2022

description:
Library name: J2_349
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_349


title: kidney biopsy_NH246


title: RNA-seq, leaf, J2_282, chemical fertilizer, Year 2022

description:
Library name: J2_282
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_282


title: kidney biopsy_NH245


title: RNA-seq, leaf, J2_318, chemical fertilizer, Year 2022

description:
Library name: J2_318
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_318


title: RNA-seq, leaf, J2_334, chemical fertilizer, Year 2022

description:
Library name: J2_334
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_334


title: UVA061  Coronary artery bulk ATAC

description: UVA061 _ATAC


title: UVA060  Coronary artery bulk ATAC

description: UVA060 _ATAC


title: RNA-seq, leaf, J2_346, chemical fertilizer, Year 2022

description:
Library name: J2_346
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_346


title: UVA058  Coronary artery bulk ATAC

description: UVA058 _ATAC


title: RNA-seq, leaf, J2_385, chemical fertilizer, Year 2022

description:
Library name: J2_385
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_385


title: RNA-seq, leaf, J2_288, chemical fertilizer, Year 2022

description:
Library name: J2_288
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_288


title: kidney biopsy_NH244


title: RNA-seq, leaf, J2_404, chemical fertilizer, Year 2022

description:
Library name: J2_404
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_404


title: kidney biopsy_NH242


title: UVA057  Coronary artery bulk ATAC

description: UVA057 _ATAC


title: kidney biopsy_NH243


title: kidney biopsy_NH247


title: RNA-seq, leaf, J2_397, chemical fertilizer, Year 2022

description:
Library name: J2_397
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_397


title: RNA-seq, leaf, J2_410, chemical fertilizer, Year 2022

description:
Library name: J2_410
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_410


title: RNA-seq, leaf, J2_362, chemical fertilizer, Year 2022

description:
Library name: J2_362
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_362


title: RNA-seq, leaf, J2_325, chemical fertilizer, Year 2022

description:
Library name: J2_325
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_325


title: RNA-seq, leaf, J2_293, chemical fertilizer, Year 2022

description:
Library name: J2_293
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_293


title: RNA-seq, leaf, J2_403, chemical fertilizer, Year 2022

description:
Library name: J2_403
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_403


title: UVA053  Coronary artery bulk ATAC

description: UVA053 _ATAC


title: kidney biopsy_NH241


title: RNA-seq, leaf, J2_395, chemical fertilizer, Year 2022

description:
Library name: J2_395
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_395


title: UVA052  Coronary artery bulk ATAC

description: UVA052 _ATAC


title: RNA-seq, leaf, J2_378, chemical fertilizer, Year 2022

description:
Library name: J2_378
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_378


title: RNA-seq, leaf, J2_416, chemical fertilizer, Year 2022

description:
Library name: J2_416
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_416


title: kidney biopsy_NH240


title: UVA056  Coronary artery bulk ATAC

description: UVA056 _ATAC


title: UVA051  Coronary artery bulk ATAC

description: UVA051 _ATAC


title: kidney biopsy_NH238


title: RNA-seq, leaf, J2_417, chemical fertilizer, Year 2022

description:
Library name: J2_417
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_417


title: RNA-seq, leaf, J2_391, chemical fertilizer, Year 2022

description:
Library name: J2_391
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_391


title: RNA-seq, leaf, J2_330, chemical fertilizer, Year 2022

description:
Library name: J2_330
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_330


title: kidney biopsy_NH237


title: RNA-seq, leaf, J2_372, chemical fertilizer, Year 2022

description:
Library name: J2_372
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_372


title: kidney biopsy_NH239


title: RNA-seq, leaf, J2_379, chemical fertilizer, Year 2022

description:
Library name: J2_379
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_379


title: RNA-seq, leaf, J2_381, chemical fertilizer, Year 2022

description:
Library name: J2_381
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_381


title: UVA050  Coronary artery bulk ATAC

description: UVA050 _ATAC


title: kidney biopsy_NH236


title: kidney biopsy_NH234


title: RNA-seq, leaf, J2_413, chemical fertilizer, Year 2022

description:
Library name: J2_413
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_413


title: UVA047  Coronary artery bulk ATAC

description: UVA047 _ATAC


title: kidney biopsy_NH235


title: UVA049  Coronary artery bulk ATAC

description: UVA049 _ATAC


title: kidney biopsy_NH233


title: RNA-seq, leaf, J2_418, chemical fertilizer, Year 2022

description:
Library name: J2_418
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_418


title: UVA046  Coronary artery bulk ATAC

description: UVA046 _ATAC


title: RNA-seq, leaf, J2_412, chemical fertilizer, Year 2022

description:
Library name: J2_412
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_412


title: kidney biopsy_NH232


title: RNA-seq, leaf, J2_304, chemical fertilizer, Year 2022

description:
Library name: J2_304
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_304


title: UVA044  Coronary artery bulk ATAC

description: UVA044 _ATAC


title: RNA-seq, leaf, J2_389, chemical fertilizer, Year 2022

description:
Library name: J2_389
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_389


title: RNA-seq, leaf, J2_314, chemical fertilizer, Year 2022

description:
Library name: J2_314
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_314


title: kidney biopsy_NH231


title: RNA-seq, leaf, J2_323, chemical fertilizer, Year 2022

description:
Library name: J2_323
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_323


title: kidney biopsy_NH230


title: RNA-seq, leaf, J2_317, chemical fertilizer, Year 2022

description:
Library name: J2_317
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_317


title: FIL_ATACSeq_REP3

city: Austin

first: TASLIMA

middle: E.

last: HAQUE

state: TX

address: J.T. Patterson Laboratories Bldg, 2415 Speedway

department: Department of Integrative Biology

institute: University of Texas at Austin

description:
Library name: FIL_ATACSeq_REP3
ATACSeq_Control

data_processing:
TAGseq data was processed as descripedin Bhaskara et al. (2016).After marking duplicated reads, bigwig file was generated at 10 bp bin normalized as CPM.
For each ATACSeq library, raw reads were trimmed using Trimmomatic v0.39 for NexteraPE (2:30:10) based on clipping leading and trailing bases below quality thresholds (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15). Reads with a minimum length of 36 bp with proper pairs were retained. The reference genomes of the two study ecotypes were masked for non-mappable regions and known repeats. To identify mappable regions, the target genome was simulated by in silico fragmentation into 100 bp fragments which were mapped to reference. Only uniquely mapped regions were considered as mappable. Trimmed reads of each ATAC-Seq library were mapped against the corresponding masked reference genome using bowtie2 v2.4.4 (-X 1000 –very-sensitive –no-mixed –no-discordant), filtered for mapping quality or mapped at organelle genomes and sorted by coordinate using SAMtools v1.13. Clonal duplicates were removed by Picard v2.25. bigwig file was generated at 10 bp bin without any normalization
Assembly: var. hallii HAL2 reference genome v2.2: https://data.jgi.doe.gov/refine-download/phytozome?genome_id=591/ and var. filipes FIL2 reference genome v3.2: https://data.jgi.doe.gov/refine-download/phytozome?genome_id=495/
Supplementary files format and content: For TAGSeq data: bigwig file. Coverage was generated using CPM normalization at 10 bp bin
Supplementary files format and content: ForA TAGSeq data: bigwig file. Coverage was generated without normalization at 10 bp bin

organism: Panicum hallii var. filipes

source_name: Leaf

growth_protocol: Seeds of inland (var. hallii; HAL2 genotype) and coastal (var. filipe; FIL2 genotype) ecotypes of P. hallii were stratified and germinated in sand for each temporal block separately. Seedlings were transferred to individual 4-inch pots filled with potting media (6:1:1 homogenous mixture of Promix: Turface: Profile) on the fourth day after germination. Plants were grown in a controlled growth chamber at 28/25°C for 12hr/12hr day/night cycle and pots were arrayed in a randomized design with four replicates in each cohort.One replicate from each ecotype from a given cohort was randomly chosen for library preparation. Leaves of a whole seedling were harvested after two weeks to prepare TAGSeq and corresponding ATAC-Seq library for that given replicate

extract_protocol:
Tissue samples were flash-frozen in liquid nitrogen, stored at -80°C and later were ground into a fine powder. RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific; Cat # 15596018) following the manufacturer’s instructions.
ATAC-Seq libraries were prepared as described by Lu et al. (2016). TAGSeq libraries were prepared from 1 μg of total RNA following the protocol described by Weng et al. (2019)

value: Leaf

value: Panicum hallii var. filipes

value: Control


title: RNA-seq, leaf, J2_352, chemical fertilizer, Year 2022

description:
Library name: J2_352
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_352


title: FIL_ATACSeq_REP1

description:
Library name: FIL_ATACSeq_REP1
ATACSeq_Control


title: UVA039  Coronary artery bulk ATAC

description: UVA039 _ATAC


title: UVA041  Coronary artery bulk ATAC

description: UVA041 _ATAC


title: mdamb231_rna_si3d_hypoxia_c

city: Aurora

first: Neelanjan

last: Mukherjee

state: Colorado

address: Research Complex 1 South, 12801 E 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description: Library name: NM2025_0102

data_processing:
Adapters were trimmed with Cutadapt (Martin et al, 2011). UMIs were trimmed and collapsed using UMI-tools (Smith et al, 2017). Salmon (Patro et al, 2017) was used for quantifying transcript levels from RNA-seq and Ribo-seq libraries using GENCODEv26 transcriptome assembly. Briefly, Salmon data were imported using the tximport (Soneson et al, 2015).  Transcript expression was quantified using Salmon v1.6 (12). Quality of ribosome sequencing data, including ribosome footprint length, p-site positioning, and three-nucleotide periodicity, was assessed using Ribowaltz (Lauria et al, 2018).
Assembly: GRCh38
Supplementary files format and content: tabular file containing salmon quantification (raw reads and TPMs) for all samples

growth_protocol: Cells were cultured in incubators at 37 ℃ with 5% CO2 and ~21% O2 (atmospheric). MCF7SIX1 cells (Clone A13) (derived from human female breast cancer cells) were generated as previously described (Ford et al, 1998). The MCF7SIX1 cells were cultured Dulbecco’s High Glucose Modified Eagle Medium (DMEM, Hyclone SH30022.01), with which 10% fetal bovine serum (FBS, Corning 35-010-CV), and 2 mM L-glutamine (L-glut, Hyclone SH30034.02) were supplemented. The MDA-MB-231 cells were cultured with Dulbecco’s High Glucose Modified Eagle Medium (DMEM, Hyclone SH30022.01), with which 5% fetal bovine serum (FBS, Corning 35-010-CV), 2 mM L-glutamine (L-glut, Hyclone SH30034.02), were supplemented.

extract_protocol:
Ribosome profiling was performed as described previously with a few modifications (Calviello et al, 2016). The lysis buffer contained 100 ug/mL cycloheximide. Following lysis and clarification by centrifugation, total RNA was quantified using the Qubit RNA BR assay kit. A portion of the lysate was reserved as input sample for RNASeq preparation. Total RNA was extracted using the DirectZol RNA Microprep kit (ZYMO Research) following the manufacturer’s instructions with on-column DNase I treatment.  Ribosomal RNA was depleted from total RNA using our previously described RNaseH-based method (Baldwin et al, 2021), then input into the KAPA RNA Hyper prep RNAseq library prep kit (Roche) according to manufacturer’s instructions with dual-index adapters, followed by quality check of the final libraries by Qubit dsDNA HS assay and Tapestation High Sensitivity D1000 screentape. Libraries were pooled and submitted for paired-end 150 bp sequencing on the Illumina NovaSeq6000 platform to a depth of 40 million paired end reads per library.
The remaining lysate was used as input into the ribosome footprinting reaction with 750 U RNase I (Invitrogen Ambion). The digestion was stopped with SUPERaseIN followed by recovery of monosomes with equilibrated Microspin S-400 HR (GE) columns. Trizol LS was added to the monosome-containing elution and RNA isolated with the ZYMO Directzol microprep kit with on-column DNase I treatment. The isolated RNA was depleted of rRNA using the siTOOLs riboPOOLs kit for ribosome profiling. The samples were resolved on a 15% TBE-Urea PAGE gel and ribosome protected fragments (RPFs) 28-29 nt in size were extracted and recovered. RPFs were treated with T4-PNK then used as input into the Qiagen QIAseq miRNA library prep kit with provided single index adapters. Libraries were pooled and submitted for paired-end 150 bp sequencing on the Illumina NovaSeq 6000 S4 platform to a depth of 50 million paired end reads per library (Novogene Corporation Inc.).

treatment_protocol: To provide a hypoxic environment, cells were placed in either a modular hypoxic chamber and filled with a premixed gas comprised of 1% O2, or the cells were placed in a BioSpherix hypoxic chamber flushed with N2 and CO2 gas. The O2 and CO2 concentrations in the BioSpherix chamber were maintained at 1% and 5%, respectively, using a carbon dioxide & oxygen controller (BioSpherix). These conditions were maintained constant throughout the course of the experiments. After hypoxic incubation was completed, quick lysis (<3 min) of the cells was necessary to prevent reoxygenation from affecting our results. ON-TARGETplus siRNA SMARTPools were ordered specifically for eIF3e (cat #: L-010518-00-0010) and eIF3d (cat #: L-017556-00-0010) from Horizon Discovery. ON-TARGETplus non-targeting pool (cat # D-001810-10) was always used as a control. siRNA transfections occurred in 25% OPTIMEM Reduced serum media and 75% full growth media (cat # 31985062). siRNAs were added to the media mixture at a concentration of 7.5 nM for 5 minutes prior to the addition of 1.875 mL Lipofectamine RNAI MAX transfection reagent (cat # 13778150) per 1 mL of media. siRNA:lipofectamine mixtures were incubated for 20 minutes before adding it directly onto the cell culture overnight. siRNA knockdowns were assessed 48-72 hours after the addition of the siRNAs.  8430 and 209 were resuspended in DMSO to a working solution concentration of 20 mM. All experiments with 8430 and 209 were used at 20 mM (1:1000 dilution) with DMSO as a vehicle control.

tag: cell line

tag: cell type

value: breast cancer

value: SIX1 OE


title: UVA040  Coronary artery bulk ATAC

description: UVA040 _ATAC


title: kidney biopsy_NH228


title: UVA054  Coronary artery bulk ATAC

description: UVA054 _ATAC


title: UVA045  Coronary artery bulk ATAC

description: UVA045 _ATAC


title: mdamb231_rna_si3e_hypoxia_c

description: Library name: NM2025_0099


title: FIL_ATACSeq_REP2

description:
Library name: FIL_ATACSeq_REP2
ATACSeq_Control


title: mdamb231_rna_si3e_hypoxia_a

description: Library name: NM2025_0097


title: mdamb231_rna_si3d_hypoxia_b

description: Library name: NM2025_0101


title: mdamb231_rna_si3e_hypoxia_b

description: Library name: NM2025_0098


title: mdamb231_rna_sictrl_hypoxia_c

description: Library name: NM2025_0096


title: kidney biopsy_NH227


title: UVA037  Coronary artery bulk ATAC

description: UVA037 _ATAC


title: mdamb231_rna_sictrl_hypoxia_a

description: Library name: NM2025_0094


title: kidney biopsy_NH226


title: kidney biopsy_NH225


title: mdamb231_rna_si3d_hypoxia_a

description: Library name: NM2025_0100


title: mdamb231_rna_sictrl_hypoxia_b

description: Library name: NM2025_0095


title: kidney biopsy_NH229


title: UVA038  Coronary artery bulk ATAC

description: UVA038 _ATAC


title: UVA032  Coronary artery bulk ATAC

description: UVA032 _ATAC


title: kidney biopsy_NH224


title: mdamb231_rna_si3d_normoxia_c

description: Library name: NM2025_0093


title: UVA033  Coronary artery bulk ATAC

description: UVA033 _ATAC


title: mdamb231_rna_si3e_normoxia_c

description: Library name: NM2025_0090


title: UVA036  Coronary artery bulk ATAC

description: UVA036 _ATAC


title: kidney biopsy_NH223


title: mdamb231_rna_si3e_normoxia_b

description: Library name: NM2025_0089


title: UVA030  Coronary artery bulk ATAC

description: UVA030 _ATAC


title: UVA031  Coronary artery bulk ATAC

description: UVA031 _ATAC


title: mdamb231_rna_sictrl_normoxia_c

description: Library name: NM2025_0087


title: mdamb231_rna_si3e_normoxia_a

description: Library name: NM2025_0088


title: kidney biopsy_NH222


title: mdamb231_rna_si3d_normoxia_a

description: Library name: NM2025_0091


title: mdamb231_rna_sictrl_normoxia_b

description: Library name: NM2025_0086


title: mdamb231_ribo_si3d_hypoxia_c

description: Library name: NM2025_0084

data_processing:
Adapters were trimmed with Cutadapt (Martin et al, 2011). UMIs were trimmed and collapsed using UMI-tools (Smith et al, 2017). Salmon (Patro et al, 2017) was used for quantifying transcript levels from RNA-seq and Ribo-seq libraries using GENCODEv26 transcriptome assembly. Briefly, Salmon data were imported using the tximport (Soneson et al, 2015).  Transcript expression was quantified using Salmon v1.6 (12). Quality of ribosome sequencing data, including ribosome footprint length, p-site positioning, and three-nucleotide periodicity, was assessed using Ribowaltz (Lauria et al, 2018).
Assembly: GRCh38
Supplementary files format and content: tabular file containing salmon quantification (raw reads and TPMs) for all samples
Library strategy: Ribo-Seq


title: mdamb231_rna_sictrl_normoxia_a

description: Library name: NM2025_0085


title: UVA028  Coronary artery bulk ATAC

description: UVA028 _ATAC


title: kidney biopsy_NH218


title: kidney biopsy_NH219


title: mdamb231_ribo_si3e_hypoxia_a

description: Library name: NM2025_0079


title: mdamb231_rna_si3d_normoxia_b

description: Library name: NM2025_0092


title: UVA026  Coronary artery bulk ATAC

description: UVA026 _ATAC


title: UVA025  Coronary artery bulk ATAC

description: UVA025 _ATAC


title: kidney biopsy_NH220


title: UVA023  Coronary artery bulk ATAC

description: UVA023 _ATAC


title: mdamb231_ribo_si3d_normoxia_a

description: Library name: NM2025_0073


title: mdamb231_ribo_si3e_hypoxia_c

description: Library name: NM2025_0081


title: kidney biopsy_NH215


title: UVA027  Coronary artery bulk ATAC

description: UVA027 _ATAC


title: kidney biopsy_NH216


title: mdamb231_ribo_si3d_hypoxia_a

description: Library name: NM2025_0082


title: UVA022  Coronary artery bulk ATAC

description: UVA022 _ATAC


title: kidney biopsy_NH214


title: kidney biopsy_NH213


title: mdamb231_ribo_si3e_normoxia_c

description: Library name: NM2025_0072


title: mdamb231_ribo_si3d_hypoxia_b

description: Library name: NM2025_0083


title: kidney biopsy_NH221


title: mdamb231_ribo_si3e_normoxia_a

description: Library name: NM2025_0070


title: mdamb231_ribo_si3e_normoxia_b

description: Library name: NM2025_0071


title: kidney biopsy_NH217


title: mdamb231_ribo_sictrl_normoxia_b

description: Library name: NM2025_0068


title: mdamb231_ribo_sictrl_hypoxia_b

description: Library name: NM2025_0077


title: kidney biopsy_NH211


title: mdamb231_ribo_si3e_hypoxia_b

description: Library name: NM2025_0080


title: UVA018  Coronary artery bulk ATAC

description: UVA018 _ATAC


title: mdamb231_ribo_si3d_normoxia_c

description: Library name: NM2025_0075


title: mdamb231_ribo_sictrl_hypoxia_a

description: Library name: NM2025_0076


title: mcf7six1_rna_8430_hypoxia_a

description: Library name: NM2025_0040


title: mdamb231_ribo_si3d_normoxia_b

description: Library name: NM2025_0074


title: mcf7six1_rna_8430_hypoxia_b

description: Library name: NM2025_0041


title: UVA019  Coronary artery bulk ATAC

description: UVA019 _ATAC


title: mcf7six1_rna_8430_hypoxia_c

description: Library name: NM2025_0042


title: mdamb231_ribo_sictrl_hypoxia_c

description: Library name: NM2025_0078


title: kidney biopsy_NH209


title: UVA021  Coronary artery bulk ATAC

description: UVA021 _ATAC


title: mcf7six1_rna_dmso_hypoxia_b_2025

description: Library name: NM2025_0038


title: UVA020  Coronary artery bulk ATAC

description: UVA020 _ATAC


title: UVA012  Coronary artery bulk ATAC

description: UVA012 _ATAC


title: mdamb231_ribo_sictrl_normoxia_a

description: Library name: NM2025_0067


title: mcf7six1_rna_8430_normoxia_c

description: Library name: NM2025_0036


title: mcf7six1_rna_8430_normoxia_a

description: Library name: NM2025_0034


title: mcf7six1_rna_dmso_normoxia_c_2025

description: Library name: NM2025_0033


title: kidney biopsy_NH210


title: mcf7six1_rna_dmso_normoxia_a_2025

description: Library name: NM2025_0031


title: kidney biopsy_NH212


title: mdamb231_ribo_sictrl_normoxia_c

description: Library name: NM2025_0069


title: kidney biopsy_NH208


title: mcf7six1_rna_dmso_normoxia_b_2025

description: Library name: NM2025_0032


title: mcf7six1_ribo_8430_hypoxia_a

description: Library name: NM2025_0010


title: UVA005  Coronary artery bulk ATAC

description: UVA005 _ATAC


title: kidney biopsy_NH203


title: UVA015  Coronary artery bulk ATAC

description: UVA015 _ATAC


title: mcf7six1_rna_dmso_hypoxia_a_2025

description: Library name: NM2025_0037


title: mcf7six1_ribo_dmso_hypoxia_c_2025

description: Library name: NM2025_0009


title: mcf7six1_rna_dmso_hypoxia_c_2025

description: Library name: NM2025_0039


title: UVA011  Coronary artery bulk ATAC

description: UVA011 _ATAC


title: kidney biopsy_NH206


title: UVA001  Coronary artery bulk ATAC

description: UVA001 _ATAC


title: UVA008  Coronary artery bulk ATAC

description: UVA008 _ATAC


title: UVA014  Coronary artery bulk ATAC

description: UVA014 _ATAC


title: mcf7six1_ribo_dmso_hypoxia_a_2025

description: Library name: NM2025_0007


title: kidney biopsy_NH202


title: mcf7six1_ribo_dmso_hypoxia_b_2025

description: Library name: NM2025_0008


title: kidney biopsy_NH201


title: mcf7six1_rna_8430_normoxia_b

description: Library name: NM2025_0035


title: mcf7six1_ribo_8430_hypoxia_b

description: Library name: NM2025_0011


title: kidney biopsy_NH200


title: mcf7six1_ribo_8430_hypoxia_c

description: Library name: NM2025_0012


title: UVA007  Coronary artery bulk ATAC

description: UVA007 _ATAC


title: kidney biopsy_NH199


title: kidney biopsy_NH205


title: kidney biopsy_NH207


title: mcf7six1_ribo_8430_normoxia_b

description: Library name: NM2025_0005


title: mcf7six1_ribo_dmso_normoxia_b_2025

description: Library name: NM2025_0002


title: mcf7six1_rna_a209_normoxia_c

description: Library name: NM2023_0120


title: inVivo138

city: New York

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

institute: Columbia University

data_processing:
Assembly: List of guides and correspodning barcodes to be quantified from the R1 FASTQ files
Analysis of CRISPR data, including the identification of the signatures, was performed using Mageck software
Supplementary files format and content: Tab-separated count matrix (genes/guides in the rows and samples in the columns)

source_name: PDA Cell Line injected in mice

extract_protocol:
sgRNA-pool containing lentiviruses were transduced into Cas9 expressing KP4 and HPAFII cell lines (in presence of 8μg/ml polybrene), at an estimated MOI = 0.2. After 24h, the lentivirus containing media was removed, cells were washed with PBS, and puromycin-containing media (2μg/ml) was added to the cells for 48-72h until all control cells (not virus-infected) were dead.
Timepoint 0 was collected 7 days after the sgRNA transductions. With timepoint 0, 1/3 of cells were stored to -80C as timepoint 0, 1/3 was implanted into pancreas of the athymic mice model and the remaining 1/3 of cells were continued to culture in vitro, as a control for the in vivo screen function. For KP4 approx. 5 million cells were implanted into each mouse and for HPAFII we implanted 2 million cells per mice. Tumor formation was monitored for 29 days, followed by sacrificing the animals and tumor collections. The genomic DNA (gDNA) from the tumors were collected by using DNeasy Blood and tissue kit (Qiagen).
NGS library preparations were done in the following way: 10 μg of gDNA, theoretically corresponding to 1.5 million diploid cells, was used as PCR template in 3 parallel PCR1 reactions (3.3 μg template DNA each) using ExTaq DNA polymerase (Takara bio). After 18 cycles, the reactions were pooled. 2 μl of pooled PCR1 product was used as template for PCR2 which was run with qPCR with index primers and stopped before the amplification started to saturate. The resulting products of approx. 360 bp were gel purified (GeneJet), pooled together and Next generation sequenced.

value: PDA Cell Line injected in mice

value: HPAFII injected in mice

tag: time

value: Timepoint 1


title: UVA002  Coronary artery bulk ATAC

description: UVA002 _ATAC


title: mcf7six1_ribo_dmso_normoxia_a_2025

description: Library name: NM2025_0001


title: kidney biopsy_NH197


title: inVivo137


title: mcf7six1_rna_a209_hypoxia_c

description: Library name: NM2023_0118


title: mcf7six1_ribo_dmso_normoxia_c_2025

description: Library name: NM2025_0003


title: kidney biopsy_NH204


title: mcf7six1_ribo_8430_normoxia_c

description: Library name: NM2025_0006


title: mcf7six1_rna_dmso_normoxia_c_2023

description: Library name: NM2023_0119


title: kidney biopsy_NH198


title: mcf7six1_ribo_8430_normoxia_a

description: Library name: NM2025_0004


title: inVivo134


title: kidney biopsy_NH196


title: mcf7six1_rna_dmso_hypoxia_c_2023

description: Library name: NM2023_0117


title: mcf7six1_ribo_dmso_hypoxia_c_2023

description: Library name: NM2023_0057


title: mcf7six1_ribo_dmso_normoxia_c_2023

description: Library name: NM2023_0059


title: mcf7six1_ribo_a209_normoxia_c

description: Library name: NM2023_0060


title: kidney biopsy_NH195


title: mcf7six1_rna_a209_normoxia_b

description: Library name: NM2023_0110


title: inVivo145

value: KP4 injected in mice


title: inVivo136


title: mcf7six1_rna_dmso_normoxia_b_2023

description: Library name: NM2023_0109


title: mcf7six1_ribo_a209_normoxia_b

description: Library name: NM2023_0050


title: mcf7six1_ribo_a209_hypoxia_c

description: Library name: NM2023_0058


title: mcf7six1_ribo_dmso_normoxia_b_2023

description: Library name: NM2023_0049


title: mcf7six1_rna_dmso_hypoxia_b_2023

description: Library name: NM2023_0107


title: inVivo144


title: kidney biopsy_NH192


title: kidney biopsy_NH193


title: inVivo135


title: inVivo142


title: inVivo133


title: kidney biopsy_NH191


title: inVivo132


title: inVivo143


title: mcf7six1_ribo_dmso_hypoxia_b_2023

description: Library name: NM2023_0047


title: mcf7six1_ribo_a209_hypoxia_b

description: Library name: NM2023_0048


title: inVivo141


title: kidney biopsy_NH194


title: kidney biopsy_NH189


title: mcf7six1_rna_a209_hypoxia_b

description: Library name: NM2023_0108


title: mcf7six1_rna_a209_hypoxia_a

description: Library name: NM2023_0098


title: mcf7six1_rna_dmso_hypoxia_a_2023

description: Library name: NM2023_0097


title: inVivo140


title: KP4_LastC


title: kidney biopsy_NH188


title: mcf7six1_rna_a209_normoxia_a

description: Library name: NM2023_0100


title: mcf7six1_ribo_a209_normoxia_a

description: Library name: NM2023_0040


title: KP4_LastB


title: mcf7six1_ribo_dmso_normoxia_a_2023

description: Library name: NM2023_0039


title: mcf7six1_rna_si3e_normoxia_c

description: Library name: NM2023_0126


title: mcf7six1_rna_dmso_normoxia_a_2023

description: Library name: NM2023_0099


title: kidney biopsy_NH187


title: mcf7six1_ribo_a209_hypoxia_a

description: Library name: NM2023_0038


title: kidney biopsy_NH190


title: mcf7six1_rna_sictrl_normoxia_c

description: Library name: NM2023_0124


title: mcf7six1_rna_si3d_normoxia_c

description: Library name: NM2023_0125


title: mcf7six1_ribo_dmso_hypoxia_a_2023

description: Library name: NM2023_0037


title: KP4_LastA


title: kidney biopsy_NH186


title: mcf7six1_rna_si3e_hypoxia_c

description: Library name: NM2023_0123


title: mcf7six1_rna_si3d_hypoxia_c

description: Library name: NM2023_0122


title: HPAFII_LastC


title: mcf7six1_rna_sictrl_hypoxia_c

description: Library name: NM2023_0121


title: kidney biopsy_NH185


title: kidney biopsy_NH184


title: HPAFII_LastB


title: mcf7six1_ribo_sictrl_normoxia_c

description: Library name: NM2023_0064


title: mcf7six1_ribo_si3e_normoxia_c

description: Library name: NM2023_0066


title: HPAFII_LastA


title: kidney biopsy_NH182


title: mcf7six1_ribo_si3e_hypoxia_c

description: Library name: NM2023_0063


title: mcf7six1_ribo_si3d_normoxia_c

description: Library name: NM2023_0065


title: shP4HA2-AS1 HK-2 cells treated with TGF-β, T_AS1_3

city: Wuhan

first: Kang

last: yang

address: No. 238 Jie-Fang Avenue, Wuhan, Hubei, P.R. China

country: China

institute: Renmin Hospital of Wuhan University

description:
Library name: Samples 9
T_AS1_3

data_processing:
CLC Genomics Workbench v 11.0.1 Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Assembly: hg19
Supplementary files format and content: txt file includes gene expression of each samples

extract_protocol:
RNA was harvested using Trizol (TAKARA). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Renal cortex proximal tubules epithelial cells

value: P4HA2-AS1 Knockdown

value: TGF-β (20ng/ml), 24h


title: shP4HA2-AS1 HK-2 cells treated with TGF-β, T_AS1_2

description:
Library name: Samples 8
T_AS1_2


title: mcf7six1_ribo_si3d_hypoxia_c

description: Library name: NM2023_0062


title: KP4_TP1

value: Timepoint 0


title: GEX_TP_NUT

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Software followed by additional downstream analyses
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PDA Cell Line

extract_protocol:
UMI-bc containing lentiviral constructs were transduced into PATU8988S cell line with MOI <0.1 followed by puromycin selection. After all the non-transduced cells were dead, we seeded 8000 cells / well (multiple wells in total), followed by incubation which lasted approx. 1-2 population doublings (daughter cells were created for each UMI-BC containing cell). At this point we performed the 1st 10x chromium run (time point 1) so that 50% of the cells were used for this this initial time point run, and the remaining 50% of the cells were cultured further for the 2nd time point. The 2nd time point chromium run was done approx. 10 population doublings later.
Portion of amplified cDNA-library was re-amplified with specific ORF_BC_amplif_oligo_F & ORF_BC_amplif_R to enrich for the lineage tracing UMI-BC (the same oligos were used in the Pooled TF overexpression assay in our publication). Finally this amplified fragment was spiked in to the whole-transcriptome part of the library with estimated 10% abundance.

value: PDA Cell Line

value: Time Point 1 - Nutrient Depleted


title: kidney biopsy_NH183

value: kidney biopsy


title: shP4HA2-AS1 HK-2 cells treated with TGF-β, T_AS1_1

description:
Library name: Samples 7
T_AS1_1


title: kidney biopsy_NH181

value: ABMR/Mixed


title: mcf7six1_ribo_sictrl_hypoxia_c

description: Library name: NM2023_0061


title: mcf7six1_rna_sictrl_normoxia_b

description: Library name: NM2023_0114


title: mcf7six1_rna_si3d_normoxia_b

description: Library name: NM2023_0115


title: HK-2 cells treated with TGF-β, T3

description:
Library name: Samples 6
T3

value: WT


title: kidney biopsy_NH178


title: KA201

description: 10x Genomics

source_name: PDA Cell Lines

extract_protocol:
Single cell RNAseq data for the 7 PDA cell lines (CAPAN1, HPAFII, HS766T, KP4, MIAPACA2, PANC0403, PATU8988S)  were  generated as following: Cell lines were trypsinized and resuspended in Cell Staining Buffer (Biolegend, Cat. No. 420201) and incubated with proper Total Seq B antibodies using recommended protocol from Biolegend.
Cells were washed twice with PBS-0.5%BSA solution and mixed them together aiming at even cell numbers for each cell line.

value: PDA Cell Lines

value: Baseline


title: kidney biopsy_NH179

value: No ABMR/Mixed


title: mcf7six1_rna_si3e_normoxia_b

description: Library name: NM2023_0116

value: breast cancer

value: SIX1 OE


title: HPAFII_TP1

value: PDA Cell Line injected in mice

value: HPAFII injected in mice


title: GEX_TP2_2

description: 10x Genomics

value: Time Point 1 -  Batch 2


title: kidney biopsy_NH177


title: mcf7six1_rna_si3e_hypoxia_b

description: Library name: NM2023_0113


title: HK-2 cells treated with TGF-β, T2

description:
Library name: Samples 5
T2

value: Renal cortex proximal tubules epithelial cells


title: GEX_TP2_1

description: 10x Genomics

value: Time Point 1 -  Batch 1


title: GEX_TP1_2

description: 10x Genomics

value: Time Point 0 - Batch 2


title: HK-2 cells treated with TGF-β, T1

description:
Library name: Samples 4
T1

value: TGF-β (20ng/ml), 24h


title: Control HK-2 cells,N3

description:
Library name: Samples 3
N3


title: Control HK-2 cells,N2

description:
Library name: Samples 2
N2


title: kidney biopsy_NH176


title: mcf7six1_rna_sictrl_hypoxia_b

description: Library name: NM2023_0111


title: mcf7six1_ribo_si3d_normoxia_b

description: Library name: NM2023_0055


title: KA951

description:
KP4 injected in mice
10x Genomics

extract_protocol:
In vivo assays were performed similarly to in vitro overexpression assays. However, only constructs for OVOL2, HNF1A, mCherry and the OVOL2-HNF1A combination were used in vivo. These viral constructs were transduced into KP4 cells in arrayed fashion (approx. MOI 1-2), followed by puromycin selections and pooling the samples together in the following ratios based on their in vitro growth rate (OVOL2 50%, HNF1A 16.6%, mCherry 16.6% and OVOL2-HNF1A 16.6%). Pooled cells were then injected into athymic mice models (3 mice in total). 14 days later the animals were sacrificed followed by scRNA-seq for the pooled samples.
Similarly, as with the pooled in vitro assays, the ORFs for any given cell were identified by using ORF barcodes and specific primers for amplifying ORF barcodes (same as with in vitro assays) from the amplified cDNA. M2RTTA was not used for in vivo overexpression assays.

value: OVOL2 - HNF1A ectopic expression


title: mcf7six1_ribo_si3e_normoxia_b

description: Library name: NM2023_0056


title: kidney biopsy_NH174


title: KA950

description:
KP4 injected in mice
10x Genomics


title: kidney biopsy_NH175


title: GEX_TP1_1

description: 10x Genomics

value: PDA Cell Line

value: Time Point 0 - Batch 1


title: mcf7six1_ribo_sictrl_normoxia_b

description: Library name: NM2023_0054


title: PK45H_TP_last_Rep1_S7_L002

data_processing: FASTQ files were counted and analyzed using MAGeCK version 0.5.6, using RRA and total read count normalization, with default settings

source_name: PK45H cell line

growth_protocol: sgRNA containing lentiviruses were transduced into Cas9 expressing PDA cell lines (HPAFII, PATU8988S, CAPAN1, KP4, PANC1, PK45H and PANC0403) in duplicates (in presence of 8ug/ml polybrene) with estimated MOI 0.2 - 0.3. Next day the lentivirus containing media was removed, cells washed with PBS and puromycin containing media (2ug/ml) was added to the cells for 48-72h until the control cells (no virus) were dead. The first timepoint of the screen was done immediately after this. At all times the cells were maintained at >1500 cells per guide through the 33-day screens

extract_protocol:
After the screen, the genomic DNA from the first and the last timepoint were extracted by using Blood and Cell culture DNA Maxi kits (Qiagen)
Library preparations were done as (PMID 30202008).
The resulting products of 290 bp were gel purified (GeneJet), pooled together and sequenced with a custom primer (CRISPRSeq) and the i5 and i7 index primers by running 20 + 6 + 6 cycles on the Illumina HiSeq2500, where i7 reads the RSL and i5 the illumina sample index.

value: PDA tumor

tag: time point

value: Last time point

tag: replicate

value: Replicate 1


title: KA952

description:
KP4 injected in mice
10x Genomics


title: kidney biopsy_NH170

value: kidney biopsy


title: kidney biopsy_NH173

value: No ABMR/Mixed


title: AM011: T1

description: 10x Genomics

extract_protocol:
UMI-bc containing lentiviral constructs were transduced into KP4 cell line with MOI <0.1 followed by puromycin selection. After all the non-transduced cells were dead, we seeded 8000 cells / well (multiple wells in total), followed by incubation which lasted approx. 1-2 population doublings (daughter cells were created for each UMI-BC containing cell). At this point we performed the 1st 10x chromium run (time point 1) so that 50% of the cells were used for this this initial time point run, and the remaining 50% of the cells were cultured further for the 2nd time point. The 2nd time point chromium run was done approx. 10 population doublings later.
scRNA-seq based bar-coded lineage tracing
Portion of amplified cDNA-library was re-amplified with specific ORF_BC_amplif_oligo_F & ORF_BC_amplif_R to enrich for the lineage tracing UMI-BC (the same oligos were used in the Pooled TF overexpression assay in our publication). Finally this amplified fragment was spiked in to the whole-transcriptome part of the library with estimated 10% abundance.

value: Time Point 1


title: kidney biopsy_NH180

value: ABMR/Mixed


title: kidney biopsy_NH172


title: kidney biopsy_NH171


title: PK45H_TP_last_Rep2_S8_L002

value: Replicate 2


title: kidney biopsy_NH168


title: PK45H_TP1_Rep1_S3_L002

value: Time point 1


title: PATU8988S_TP_last_replica2_S12

source_name: PATU8988S cell line


title: mcf7six1_ribo_sictrl_hypoxia_b

description: Library name: NM2023_0051

value: breast cancer

value: SIX1 OE


title: EAC, Fresh-frozen, Sample 20

city: Oxford

first: Eileen

last: Parkes

address: Off Roosevelt Drive

department: Department of Oncology

country: United Kingdom

institute: University of Oxford

description:
Library name: 20_EAC_CIN_TME
Sample identifier in the CIN_TME_EAC.rds Seurat object metadata column (orig.ident): 20-EAC-CIN-TME

data_processing:
Raw snRNA-seq FASTQ files were processed using Cell Ranger (v.6.0.0, 10x Genomics). Reads were aligned to the human GRCh38 reference genome and gene counts were quantified using Cell Ranger, with intronic reads included to account for nuclear mRNA.  Ambient RNA and empty droplets were removed from raw gene expression matrices using CellBender (v.0.2.0) applied to Cell Ranger–generated raw feature-barcode matrices. The expected number of cells was defined using Cell Ranger estimates, and the total number of droplets included was determined based on inspection of barcode-rank plots.  Filtered expression matrices were analyzed in R using Seurat (v.4.2.7). Nuclei with 200–9,000 detected genes, 800–40,000 UMIs, and <15% mitochondrial reads were retained. Doublets were identified and removed using Scrublet (v.0.2.1).
Assembly: GRCh38
Supplementary files format and content: Seurat objects (.rds) of Cell Ranger outputs for each sample. An integrated Seurat object (CIN_TME_EAC.rds) comprising all samples, where the "orig.ident" metadata column corresponds to sample library names.

molecule: nuclear RNA

source_name: Esophageal adenocarcinoma, Gastroesophageal junction (Siewert 1)

extract_protocol:
Clinical-grade frozen esophageal adenocarcinoma (EAC) tissue samples were collected under Oxford Radcliffe Biobank-approved study 21/A093 with informed patient consent. To enable tissue-sparing single-nucleus RNA sequencing (snRNA-seq), nuclei were isolated using an optimized salt-tris (ST)-based extraction protocol adapted for EAC specimens. Frozen tissues embedded in OCT were cryosectioned at –20°C using a Leica CM1950 cryostat, generating 40–60 scrolls of 20 μm thickness per sample. Processing steps were performed on ice using pre-chilled buffers. OCT was removed by PBS washes, followed by mechanical dissociation in ST buffer supplemented with Tween-20 and BSA. Homogenates were quenched with RNase inhibitor, sequentially filtered, and centrifuged to enrich nuclei. Final nuclear suspensions were stained with Hoechst and quantified by fluorescence microscopy prior to downstream snRNA-seq library preparation.
Approximately 14,000 nuclei were loaded per sample onto a Chromium X instrument (10x Genomics), with the exception of sample #5 for which ~7,600 nuclei were used. Nuclei were suspended in ST buffer and processed using the Chromium Next GEM Single Cell 5′ Kit v2 following the manufacturer’s protocol. Gel bead-in-emulsions (GEMs) underwent reverse transcription, Dynabeads-based cleanup, and cDNA amplification, with one additional PCR cycle included (14 total cycles) to account for reduced RNA content in nuclei. Gene expression (GEX) libraries were constructed using the 10x Genomics Library Construction and Dual Index kits according to the user guide. cDNA and final library fragment size distributions were assessed using an Agilent TapeStation 2200, and library concentrations were quantified using a Qubit fluorometer.  Final GEX libraries were sequenced on an Illumina NovaSeq X Plus platform using a paired-end 150 bp configuration, achieving ≥20,000 read pairs per nucleus. Sequencing was performed with a 26–10–10–90 cycle setup for read 1, i7 index, i5 index, and read 2, respectively, with a 2% PhiX spike-in included as an internal sequencing control.


title: kidney biopsy_NH169


title: PK45H_TP1_Rep2_S4_L002


title: Control HK-2 cells,N1

description:
Library name: Samples 1
N1

value: Renal cortex proximal tubules epithelial cells

value: WT


title: MT002B: T1 - Batch 2

description: 10x Genomics

extract_protocol:
UMI-bc containing lentiviral constructs were transduced into Hs766T cell line with MOI <0.1 followed by puromycin selection. After all the non-transduced cells were dead, we seeded 8000 cells / well (multiple wells in total), followed by incubation which lasted approx. 1-2 population doublings (daughter cells were created for each UMI-BC containing cell). At this point we performed the 1st 10x chromium run (time point 1) so that 50% of the cells were used for this this initial time point run, and the remaining 50% of the cells were cultured further for the 2nd time point. The 2nd time point chromium run was done approx. 10 population doublings later.
Portion of amplified cDNA-library was re-amplified with specific ORF_BC_amplif_oligo_F & ORF_BC_amplif_R to enrich for the lineage tracing UMI-BC (the same oligos were used in the Pooled TF overexpression assay in our publication). Finally this amplified fragment was spiked in to the whole-transcriptome part of the library with estimated 10% abundance.
scRNA-seq based bar-coded lineage tracing


title: AM010: T0

description: 10x Genomics

value: Time Point 0


title: PATU8988S_TP_last_replica1_S11


title: H766TP1B: T0 - Batch 2

description: 10x Genomics


title: kidney biopsy_NH166


title: EAC, Fresh-frozen, Sample 17

description:
Library name: 17_EAC_CIN_TME
Sample identifier in the CIN_TME_EAC.rds Seurat object metadata column (orig.ident): 17_EAC_CIN_TME

source_name: Esophageal adenocarcinoma, Gastroesophageal junction (Siewert 2)


title: H766TP1A: T0 - Batch 1

description: 10x Genomics


title: EAC, Fresh-frozen, Sample 18

description:
Library name: 18_EAC_CIN_TME
Sample identifier in the CIN_TME_EAC.rds Seurat object metadata column (orig.ident): 18_EAC_CIN_TME

value: Esophageal adenocarcinoma, Gastroesophageal junction (Siewert 2)


title: kidney biopsy_NH167


title: PATU8988S_TP1_replica1_S5


title: kidney biopsy_NH164


title: EAC, Fresh-frozen, Sample 10

description:
Library name: 10_EAC_CIN_TME
Sample identifier in the CIN_TME_EAC.rds Seurat object metadata column (orig.ident): 10_EAC_CIN_TME

value: Esophageal adenocarcinoma, Gastroesophageal junction (Siewert 1)


title: PANC1_TP_last_replica2_S10

source_name: PANC1 cell line


title: PATU8988S_TP1_replica2_S6


title: kidney biopsy_NH163


title: EAC, Fresh-frozen, Sample 16

description:
Library name: 16_EAC_CIN_TME
Sample identifier in the CIN_TME_EAC.rds Seurat object metadata column (orig.ident): 16-EAC-CIN-TME


title: KA001: KP4, PK45H, PANC1

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Software and CITE-Seq count
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: KP4, PK45H, PANC1

growth_protocol: A digestion buffer that contained trypsin, DNAse and enzymatic cocktail (Miltenyi, Cat. No. 130-095- 929) and the gentleMACS Octo Dissociator (Milteny Biotec, Cat. No. 130-095-937) were made for initial tumor disruption using manufacture’s protocol. Cell suspensions were then filtered using a 40μm cell strainer (Falcon, Cat. No. 352340) and red blood cells (RBC) were removed by RBC lysis buffer (Invitrogen, Cat. No. 1966634)

extract_protocol:
Dissociated cells were washed twice with PBS 0.1% BSA buffer with cold centrifuging at 500rpm and 5’. Finally, cells were stained with 0.4% Trypan blue (Invitrogen, Cat. No. T10282) to check the viability and diluted with PBS 0.1% BSA to about 1E106 cells/ml for single cell sequencing. For each single cell run, 6 samples were combined
Dissociated cells were processed for single-cell gene expression capture (scRNA-seq) using the 10X Chromium 3’ Library and Gel Bead Kit (10x Genomics), following the manufacturer’s user guide.
Libraries were prepared following the manufacturer’s user guide and sequenced at the Columbia University Single Cell Analysis Core

treatment_protocol: Normal and Serum-free media

value: PDA Cell Lines

value: KP4, PK45H, PANC1

value: Normal and Serum-Free media


title: kidney biopsy_NH165


title: EAC, Fresh-frozen, Sample 6

description:
Library name: 6_EAC_CIN_TME
Sample identifier in the CIN_TME_EAC.rds Seurat object metadata column (orig.ident): 6_EAC_CIN_TME

source_name: Esophageal adenocarcinoma, Esophagus (Lower 1/3)


title: Untreated single-cells

data_processing:
FASTQ files and the UMI-count matrix were generated using the Cell Ranger pipeline version 3.1.0 and we detect and remove suspected index swap contaminant reads as described in "Griffiths JA, Richard AC, Bach K, Lun ATL, Marioni JC. Detection and removal of barcode swapping in single-cell RNA-seq data. Nat Commun. 2018;9(1):2667. Published 2018 Jul 10. doi:10.1038/s41467-018-05083-x
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: Table containing UMI count of each gene (row) in each cell (column)

source_name: PDAC tumor

growth_protocol: PDAC tumor was ortothopically injected into NRG mice and tumor volume was measured by ultrasounds twice weekly.

extract_protocol:
Single cells were obtained after digestion, filtering and multiple washes from PDAC tumors.
We used the Chromium Single Cell 3ʹ Reagent Kits v3. We did 12 cycles for cDNA amplification and 12 for library amplification

tag: mouse strain

value: NRG

value: Pancreatic Ductal Adenocarcinoma

value: Untreated


title: PANC1_TP_last_replica1_S9

value: PDA tumor

value: Last time point

value: Replicate 1


title: PANC1_TP1_replica2_S4

value: Time point 1

value: Replicate 2


title: EAC, Fresh-frozen, Sample 5

description:
Library name: 5_EAC_CIN_TME
Sample identifier in the CIN_TME_EAC.rds Seurat object metadata column (orig.ident): 5_EAC_CIN_TME

value: Esophageal adenocarcinoma, Esophagus (Lower 1/3)


title: AM007

data_processing:
Reads were processed with Kallisto pipeline using GRCh38 as reference
Genome_build: GRCh38
Supplementary_files_format_and_content: Table containing read count of each gene (row) in each sample (column)

growth_protocol: PDA cell lines were cultured in 6-well format so that at the time of RNA extractions the cell confluency was always < 50% and cells were seeded to the well at least 48-72h before cell lysis

extract_protocol:
Total RNA was extracted by using RNeasy Plus mini kit (Qiagen)
Samples were sequenced by using NovaSeq 6000 (PE 20million reads).


title: OverExpression

data_processing:
Reads were processed with Cell Ranger Version pipeline (3.0.2) using GRCh38 as reference
Genome_build: GRCh38
Supplementary_files_format_and_content: Table containing read count of each gene (row) in each sample (column)

source_name: HPAFII/PATU8988S/KP4 cell line

growth_protocol: All the ORF viruses were pooled into two viral pools so that on average 2-3 ORFs enter each cell (MOI 0.288 / each virus)in a random fashion. M2RTTA was added to the other pool to increase the transcriptional outputof the ORFs in that pool. KP4 cells were transduced with these two viral pools in 6 well formatwith   the   presence   of   polybrene.   The   following   day   media   was   changed   and   puromycin(2.5ug/ml) and doxocycline (0.6ug/ml) was added to the cells

extract_protocol:
The   cells   were   incubated   in   total   11   days,   before   trypsinization,   addition   Multiseq   barcodes(PMID:   31209384)   and   chromium-run.   Non-transduced   KP4,   HPAFII   and   PATU8988S   cellswere   also   included   into   this   stage   of   the   protocol   to   act   as   assay   starting   population(morphogenic  cell line KP4) and assay target end point population  (lineage cell lines HPAFIIand PATU8988S).
All the cell lines (normal KP4, HPAFII, PATU8988S and KP4 assay pools +/-M2rtTA) were MultiSeq barcoded and mixed prior the Chromium-run.

value: Untreated/Overexpressed MRs


title: kidney biopsy_NH160

value: No ABMR/Mixed

value: kidney biopsy


title: kidney biopsy_NH161


title: EAC, Fresh-frozen, Sample 3

description:
Library name: 3_EAC_CIN_TME
Sample identifier in the CIN_TME_EAC.rds Seurat object metadata column (orig.ident): 3_EAC_CIN_TME


title: kidney biopsy_NH162


title: EAC, Fresh-frozen, Sample 1

description:
Library name: 1_EAC_CIN_TME
Sample identifier in the CIN_TME_EAC.rds Seurat object metadata column (orig.ident): 1-EAC-CIN-TME


title: PANC1_TP1_replica1_S3


title: AM004


title: KP4_TP_last_replica2_S8

source_name: KP4 cell line


title: AM005

source_name: CAPAN1 cell line


title: AM003


title: KP4_TP_last_replica1_S7


title: KP4_TP1_replica2_S2


title: kidney biopsy_NH159

value: ABMR/Mixed


title: KP4_TP1_replica1_S1


title: OCIAML3 LTR12C KD CUT&RUN H3K27ac R1

city: London

first: Ozgen

last: Deniz

state: Greater London

address: Charterhouse square

institute: Barts Cancer Institute

description: Library name: Sample15

data_processing:
Sequences were trimmed with TrimGalore and aligned to the T2T reference genome using bowtie2,
generating SAM files. An in-house perl script was used to get uniquely aligned reads. SAMtools was
used to mate paired reads, remove duplicates, and index bam files for analysis. Peak calling for ATAC-seq and CUT&RUN data was achieved with MACS2, taking peaks with a p cutoff of 0.01 for atac and p = 0.05, for CUT&RUN, using BAMPE option.
bigWig files were generated using genomicRanges R package.
Assembly: T2T
Supplementary files format and content: bigwig
Library strategy: CUT&Run

growth_protocol: OCIAML3 cells were kept in RPMI +10% FBS, supplemented with 1x antimicrobial antimycobacterial and 1x GlutaMAX.

extract_protocol:
500000 live cells per reaction were pelleted and digestion was carried out with pAG-MNase following the kit manufacturer’s protocol (75).
Library preparation was  carried out per the NEBNext Ultra II DNA Library Prep Kit for Illumina.5-10ng
of DNA was used as starting material and libraries were amplfied using 13 cycles on thermocycler. Libraries were quality assessed using D1000 DNA screen tapes on an agilent 4200 TapeStation. Libraries were sent for Novaseq sequencing.

value: AML

value: LTR12C CRISPRi


title: kidney biopsy_NH158

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).


title: OCIAML3  ctrl CUT&RUN H3K27ac R2

description: Library name: Sample14

value: Control


title: kidney biopsy_NH157


title: AM002


title: AM001

source_name: HPAFII cell line

value: HPAFII


title: OCIAML3 ctrl CUT&RUN H3K27ac R1

description: Library name: Sample13


title: HPAFII_TP_last_Rep2_S6_L002


title: kidney biopsy_NH156

source_name: kidney biopsy


title: OCIAML3 LTR12C KD CUT&RUN H3K9me3 R2

description: Library name: Sample12


title: kidney biopsy_NH155


title: HPAFII_TP_last_Rep1_S5_L002


title: kidney biopsy_NH154


title: shKDM2A_Cluster_Input_Rep3

city: New Haven

first: Don

last: Nguyen

state: Connecticut

address: 310 Cedar Street

department: Pathology

institute: Yale University

description: Library name: CK100

data_processing:
All samples were quality controlled using FastQC (Babraham Bioinformatics).
Narrow peaks (H3K27Ac, FLAG-KDM2A) were trimmed with TrimGalore (Babraham Bioinformatics) and FLAG-KDM2A reads were cleaned with SMARTCleaner. Broad peaks (H3K36me) were trimmed Trimmomatic. Experiments were aligned against hg38 using Bowtie2.
Peak calling was done using MACS2 (narrow) and MACS3 (broad).
Average coverage files were generated using deepTools tools: bamCoverage, bigwigAverage, and bigwigCompare. Prior to generation, optical duplicates were removed using Picard Tools (Broad Institute), and poor-quality reads filtered using samTools20. All coverage files were normalized for sequencing depth using the counts per million (CPM) method, and averaged using bigwigAverage.
Assembly: hg38
Supplementary files format and content: Average BigWig files of CPM normalized reads for each methylation IP  are provided. MACS2 called peaks are provided for FLAG samples.

growth_protocol: H2030-BrM3 cells were grown  under cluster forming conditions in the presence of doxycycline for 5 days.

extract_protocol:
H3K27Ac: Samples were sent to Active Motif (Carlsbad, CA) for ChIP-Seq. Active Motif prepared chromatin, performed ChIP reactions, generated libraries, sequenced the libraries and performed basic data analysis. In brief, cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Qubit. Extrapolation to the original chromatin volume allowed determination of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4ug of antibody against H3K27Ac (Active Motif, catalog number 39133, lot number 06921014). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.   FLAG and H3K36Me: FLAG-KDM2A samples were double-fixed using 2mM ethylene glycol bis(scuccinimidyl succinate) (EGS) (Thermo Scientific cat. 21565) for 1h followed by 1% formaldehyde for ten minutes.  H3K36 methylation samples were fixed with 1% formaldehyde alone.  Reactions were quenched with glycine to a final concentration of 0.125M. Pellets were washed with PBS and lysed in complete sonication buffer (20mM Tris pH 8.0, 2mM EDTA, 0.5mM EGTA, 1x protease inhibitors (Roche), 0.5% SDS, and 0.5mM PMSF) prior to sonication with a QSonica Q800. Fragment size (200-500bp) from extracted DNA was confirmed by agarose gel and quantified by Qubit. Input was aliquoted from 20% of total material, and chromatin samples were subsequently pre-cleared for 1 hour at 4ºC with immunoprecipitation (IP) buffer (20mM Tris pH 8.0, 2mM EDTA, 0.5% Triton X-100, 150mM NaCl, and 10% Glycerol) and Protein A/G beads. IP for proteins of interest was conducted using protein A/G beads and 10µg of antibody. For H3K36 methylation IPs Drosophila spike-in chromatin (100ng)  (Active Motif cat. 53083) and spike-in antibody (5μg) (Active Motif cat. 61686)were added. IPs were washed then eluted in a buffer of 100mM NaHC03, 1% SDS. Both IP and input samples were proteinase K treated, reverse crosslinked, and purified by phenol-chloroform extraction with ethanol precipitation.
H3K27Ac: Illumina sequencing libraries (a custom type, using the same paired read adapter oligonucleotides described by Bentley et al., 2008)) were prepared from the ChIP and Input DNAs on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500  (75 nt reads, single end).  FLAG and H3K36Me: Samples were checked by Agilent Bioanalyzer, and libraries were prepared by the using ThruPlex DNA Seq (Takara Bio. cat. R400674) for H3K36 libraries, and DNA SMART ChiP-Seq (Takara Bio.cat. 634865) for FLAG libraries. Libraries were barcoded, pooled, and sequenced (PE) on Illumina NovaSeq X and NovaSeq 6000 machines. Please note, H3K36 methylation libraries were  initially sequenced on the NovaSeq 6000 then subsequently on the NovaSeq X  for additional coverage depth. Fastq files from these runs were concatinated head to tail prior to any anaylsis, and these pooled files are provided here for convenience. Files from each individual sequencing run are available upon request.

value: Human metastatic lung adenocarcinoma


title: OCIAML3 LTR12C KD CUT&RUN H3K9me3 R1

description: Library name: Sample11


title: shKDM2A_Cluster_Input_Rep4

description: Library name: CK220


title: HPAFII_TP1_Rep2_S2_L002


title: KA002: MIAPACA2, PATU8902, SW1990

description: 10x Genomics

source_name: MIAPACA2, PATU8902, SW1990

value: PDA Cell Lines

value: MIAPACA2, PATU8902, SW1990

value: Normal and Serum-Free media


title: OCIAML3  ctrl CUT&RUN H3K9me3 R2

description: Library name: Sample10


title: OCIAML3 ctrl CUT&RUN H3K9me3 R1

description: Library name: Sample9


title: HPAFII_TP1_Rep1_S1_L002

value: PDA tumor


title: shKDM2A_Cluster_Input_Rep2

description: Library name: CK180


title: shKDM2A_Cluster_Input_Rep1

description: Library name: CK40


title: kidney biopsy_NH151


title: kidney biopsy_NH152


title: kidney biopsy_NH153


title: shControl_Cluster_Input_Rep4

description: Library name: CK210


title: OCIAML3 LTR12C KD CUT&RUN IgG R2

description: Library name: Sample8


title: CAPAN1_TP_last_R1_S7

value: Last time point

value: Replicate 1


title: CAPAN1_TP_last_R2_S8

value: Replicate 2


title: CAPAN1_TP1_R2_S6

value: Time point 1


title: shControl_Cluster_Input_Rep3

description: Library name: CK90


title: CAPAN1_TP1_R1_S5


title: mcf7six1_ribo_si3d_hypoxia_b

description: Library name: NM2023_0052

extract_protocol:
Ribosome profiling was performed as described previously with a few modifications (Calviello et al, 2016). The lysis buffer contained 100 ug/mL cycloheximide. Following lysis and clarification by centrifugation, total RNA was quantified using the Qubit RNA BR assay kit. A portion of the lysate was reserved as input sample for RNASeq preparation. Total RNA was extracted using the DirectZol RNA Microprep kit (ZYMO Research) following the manufacturer’s instructions with on-column DNase I treatment.  Ribosomal RNA was depleted from total RNA using our previously described RNaseH-based method (Baldwin et al, 2021), then input into the KAPA RNA Hyper prep RNAseq library prep kit (Roche) according to manufacturer’s instructions with dual-index adapters, followed by quality check of the final libraries by Qubit dsDNA HS assay and Tapestation High Sensitivity D1000 screentape. Libraries were pooled and submitted for paired-end 150 bp sequencing on the Illumina NovaSeq6000 platform to a depth of 40 million paired end reads per library.
The remaining lysate was used as input into the ribosome footprinting reaction with 750 U RNase I (Invitrogen Ambion). The digestion was stopped with SUPERaseIN followed by recovery of monosomes with equilibrated Microspin S-400 HR (GE) columns. Trizol LS was added to the monosome-containing elution and RNA isolated with the ZYMO Directzol microprep kit with on-column DNase I treatment. The isolated RNA was depleted of rRNA using the siTOOLs riboPOOLs kit for ribosome profiling. The samples were resolved on a 15% TBE-Urea PAGE gel and ribosome protected fragments (RPFs) 28-29 nt in size were extracted and recovered. RPFs were treated with T4-PNK then used as input into the Qiagen QIAseq miRNA library prep kit with provided single index adapters. Libraries were pooled and submitted for paired-end 150 bp sequencing on the Illumina NovaSeq 6000 S4 platform to a depth of 50 million paired end reads per library (Novogene Corporation Inc.).

value: breast cancer

value: SIX1 OE


title: shControl_Cluster_Input_Rep2

description: Library name: CK170


title: OCIAML3  ctrl CUT&RUN IgG R2

description: Library name: Sample6


title: kidney biopsy_NH148

value: No ABMR/Mixed

value: kidney biopsy


title: shControl_Cluster_Input_Rep1

description: Library name: CK20


title: OCIAML3 ctrl CUT&RUN IgG R1

description: Library name: Sample5

value: AML


title: kidney biopsy_NH147


title: kidney biopsy_NH149


title: PK45H_TP_last_Rep2_S8_L001_R1_001

data_processing:
FASTQ files were counted and analyzed using MAGeCK version 0.5.6, using RRA and total read count normalization, with default settings
Supplementary_files_format_and_content: counts_table_CRIPSR.csv

growth_protocol: sgRNA containing lentiviruses were transduced into Cas9 expressing PDA cell lines (HPAFII, PATU8988S, CAPAN1, KP4, PANC1 and PK45H) in duplicates (in presence of 8ug/ml polybrene) with estimated MOI 0.2 - 0.3. Next day the lentivirus containing media was removed, cells washed with PBS and puromycin containing media (2ug/ml) was added to the cells for 48-72h until the control cells (no virus) were dead. The first timepoint of the screen was done immediately after this. At all times the cells were maintained at >1500 cells per guide through the 33-day screens

value: Last time point / Replicate 2


title: kidney biopsy_NH150

value: ABMR/Mixed


title: shKDM2A_Control_Input_Rep4

description: Library name: CK240


title: OCIAML3 LTR12C KD CUT&RUN IgG R1

description: Library name: Sample7

value: LTR12C CRISPRi


title: OCIAML3 LTR12C KD ATAC R2

description: Library name: Sample4

data_processing:
Sequences were trimmed with TrimGalore and aligned to the T2T reference genome using bowtie2,
generating SAM files. An in-house perl script was used to get uniquely aligned reads. SAMtools was
used to mate paired reads, remove duplicates, and index bam files for analysis. Peak calling for ATAC-seq and CUT&RUN data was achieved with MACS2, taking peaks with a p cutoff of 0.01 for atac and p = 0.05, for CUT&RUN, using BAMPE option.
bigWig files were generated using genomicRanges R package.
Assembly: T2T
Supplementary files format and content: bigwig


title: PK45H_TP_last_Rep1_S7_L001_R1_001

value: Last time point / Replicate 1


title: PK45H_TP1_Rep2_S4_L001_R1_001

value: Time point 1 / Replicate 2


title: kidney biopsy_NH146

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.


title: kidney biopsy_NH145


title: shKDM2A_Control_Input_Rep2

description: Library name: CK120

value: Human metastatic lung adenocarcinoma


title: OCIAML3 ctrl ATAC R1

description: Library name: Sample1

value: Control


title: PATU8988S_TP_last_replica2_S12_R1_001

value: PDA tumor


title: PK45H_TP1_Rep1_S3_L001_R1_001

value: Time point 1 / Replicate 1


title: kidney biopsy_NH143


title: OCIAML3 LTR12C KD ATAC R1

description: Library name: Sample3


title: shKDM2A_Control_Input_Rep1

description: Library name: CK30


title: kidney biopsy_NH144


title: hSS-pro3

city: Zunyi

first: Hong-Qing

last: She

address: 6 Xuefu West Road, Honghuagang District

institute: Zunyi Medical University

description:
Library name: hSS-pro3
hSSpro3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was builtusing Hisat2 v2.0.5 and paired-end clean reads were aligned to thereference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: xls files include FPKM values for each Sample

source_name: organoid

extract_protocol:
RNA was harvested using Trizol, total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: organoid

value: Ventral forebrain organoids

value: propofol


title: shKDM2A_Control_Input_Rep3

description: Library name: CK200


title: hSS-pro2

description:
Library name: hSS-pro2
hSSpro2


title: shControl_Control_Input_Rep4

description: Library name: CK230


title: PATU8988S_TP_last_replica1_S11_R1_001


title: PATU8988S_TP1_replica2_S6_R1_001


title: shControl_Control_Input_Rep3

description: Library name: CK190


title: kidney biopsy_NH142


title: hSS-pro1

description:
Library name: hSS-pro1
hSSpro1


title: PATU8988S_TP1_replica1_S5_R1_001


title: kidney biopsy_NH141


title: MT002A: T1 - Batch 1

description: 10x Genomics

source_name: PDA Cell Line

value: PDA Cell Line

value: Time Point 1


title: shControl_Control_Input_Rep2

description: Library name: CK110


title: OCIAML3 ctrl ATAC R2

description: Library name: Sample2


title: OCIAML3 LTR12C KD CUT&RUN H3K27ac R2

description: Library name: Sample16


title: hSS3

description:
Library name: hSS3
hSS3


title: PANC1_TP_last_replica2_S10_R1_001


title: kidney biopsy_NH139


title: hSS2

description:
Library name: hSS2
hSS2


title: shControl_Control_Input_Rep1

description: Library name: CK10


title: mcf7six1_ribo_si3e_hypoxia_b

description: Library name: NM2023_0053

value: breast cancer

value: SIX1 OE


title: PANC1_TP_last_replica1_S9_R1_001


title: PANC1_TP1_replica2_S4_R1_001


title: kidney biopsy_NH140

value: No ABMR/Mixed

value: kidney biopsy


title: shKDM2A_Cluster_H3K36me3_Rep3

description: Library name: CK103


title: shKDM2A_Cluster_H3K36me3_Rep4

description: Library name: CK223


title: kidney biopsy_NH138

value: ABMR/Mixed


title: hCS-pro3

description:
Library name: hCS-pro3
hCSpro3

value: Dorsal forebrain organoids


title: hCS-pro2

description:
Library name: hCS-pro2
hCSpro2


title: kidney biopsy_NH137


title: PANC1_TP1_replica1_S3_R1_001


title: shKDM2A_Cluster_H3K36me3_Rep2

description: Library name: CK183


title: KP4_TP_last_replica2_S8_R1_001

value: Last time point / Replicate 2


title: hSS1

description:
Library name: hSS1
hSS1


title: kidney biopsy_NH136


title: hCS-pro1

description:
Library name: hCS-pro1
hCSpro1


title: hCS3

description:
Library name: hCS3
hCS3


title: KP4_TP1_replica2_S2_R1_001

value: Time point 1 / Replicate 2


title: kidney biopsy_NH135


title: KP4_TP_last_replica1_S7_R1_001

value: Last time point / Replicate 1


title: shControl_Cluster_H3K36me3_Rep3

description: Library name: CK93

value: Human metastatic lung adenocarcinoma


title: mcf7six1_rna_si3d_hypoxia_b

description: Library name: NM2023_0112

data_processing:
Adapters were trimmed with Cutadapt (Martin et al, 2011). UMIs were trimmed and collapsed using UMI-tools (Smith et al, 2017). Salmon (Patro et al, 2017) was used for quantifying transcript levels from RNA-seq and Ribo-seq libraries using GENCODEv26 transcriptome assembly. Briefly, Salmon data were imported using the tximport (Soneson et al, 2015).  Transcript expression was quantified using Salmon v1.6 (12). Quality of ribosome sequencing data, including ribosome footprint length, p-site positioning, and three-nucleotide periodicity, was assessed using Ribowaltz (Lauria et al, 2018).
Assembly: GRCh38
Supplementary files format and content: tabular file containing salmon quantification (raw reads and TPMs) for all samples


title: shKDM2A_Cluster_H3K36me3_Rep1

description: Library name: CK43


title: KP4_TP1_replica1_S1_R1_001

value: PDA tumor


title: kidney biopsy_NH132


title: shControl_Cluster_H3K36me3_Rep4

description: Library name: CK213


title: hCS1

description:
Library name: hCS1+L41A4A41:U41
hCS1


title: kidney biopsy_NH133


title: shControl_Cluster_H3K36me3_Rep2

description: Library name: CK173


title: hCS2

description:
Library name: hCS2
hCS2


title: shControl_Cluster_H3K36me3_Rep1

description: Library name: CK23


title: kidney biopsy_NH134


title: shKDM2A_Control_H3K36me3_Rep4

description: Library name: CK243


title: shKDM2A_Control_H3K36me3_Rep3

description: Library name: CK203


title: HPAFII_TP_last_Rep1_S5_L001_R1_001

value: HPAFII


title: RS_HS_Hela_Lpg1949-WT_INFb_rep1

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

institute: xiamen University

description:
Library name: Sample 3
Lpg1949-WT

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg38 genome assembly using STAR version 2.7.10.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Hela

growth_protocol: Hela cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin, and were maintained in a 5% CO2 incubator at 37°C.

extract_protocol:
Total RNA was isolated using R (Qiagen) following the manufacturer's instructions. DNase I in column digestion was included to ensure RNA quality.
RNA library preparation was performed by using NEBNext@ UItraTM Directional RNA Library Prep Kit for Illumina (E7420L) and paired-end sequencing was performed with Illumina HiSeq X Ten platform.

treatment_protocol: HeLa cells were transfected with empty vector or Lem17, and after 24 hours of expression, stimulated with 20ng/mL IFN-β for 6 hours.

value: Hela

value: WT

value: INFb


title: RS_HS_Hela_CK_INFb_rep1

description:
Library name: Sample 1
WT


title: RS_HS_Hela_CK_INFb_rep2

description:
Library name: Sample 2
WT


title: kidney biopsy_NH131


title: HPAFII_TP1_Rep1_S1_L001_R1_001

value: Time point 1 / Replicate 1


title: kidney biopsy_NH130


title: shKDM2A_Control_H3K36me3_Rep1

description: Library name: CK33


title: shKDM2A_Control_H3K36me3_Rep2

description: Library name: CK123


title: HPAFII_TP_last_Rep2_S6_L001_R1_001


title: kidney biopsy_NH129


title: HELA-NC

city: Beijing

first: Yueyue

last: Yan

state: Beijing

address: No. 1 ShuaiFuyuan Road, Dongcheng District

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

description: Library name: HELA-NC

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKMvalues for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) from roots tissue of Scutellaria baicalensis Georgi according to protocol. Then, electrophoresis on a denaturing agarose gel and NanoDrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) were used for separating and measuring total RNA. Approximately 2 µg of total RNA with a concentration of 200 ng/µl from equal amount of RNA samples.
RNA libraries created with the QIAseq miRNA Library Kit (Qiagen, Valencia, CA, USA) from total RNA following manufacturer's protocols.


title: HPAFII_TP1_Rep2_S2_L001_R1_001


title: kidney biopsy_NH128


title: CAPAN1_WT_TP_last_R1_S3_R1_001


title: RS_HS_Hela_Lpg1949-WT_INFb_rep2

description:
Library name: Sample 4
Lpg1949-WT


title: kidney biopsy_NH127


title: kidney biopsy_NH126